8W51 | pdb_00008w51

Structure of YchF(H114A) on E.coli 50S ribosomal subunit

PDB DOI: https://doi.org/10.2210/pdb8W51/pdb
EM Map EMD-37271: EMDB EMDataResource
NAKB: 8W51

Classification: RIBOSOME
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-08-25 Released: 2024-08-28
Deposition Author(s): Yu, T., Li, X., Zeng, F.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Guangdong Basic and Applied Basic Research Foundation, Shenzhen Science and Technology Program

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure basis of translation regulation by YchF bound to ribosome

Li, X., Yu, T., Li, Q., Zeng, F.

To be published.

Macromolecule Content

Total Structure Weight: 1,401.34 kDa
Atom Count: 93,901
Modeled Residue Count: 6,751
Deposited Residue Count: 6,810
Unique protein chains: 30
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	C	273	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422 Go to UniProtKB: P60422
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60422
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	D	209	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438 Go to UniProtKB: P60438
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60438
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	E	201	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723 Go to UniProtKB: P60723
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60723
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	F	179	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P62399 (Escherichia coli (strain K12)) Explore P62399 Go to UniProtKB: P62399
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62399
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	G	177	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12)) Explore P0AG55 Go to UniProtKB: P0AG55
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AG55
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	H	149	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1 Go to UniProtKB: P0A7R1
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7R1
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL11	I [auth J]	142	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12)) Explore P0A7J7 Go to UniProtKB: P0A7J7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7J7
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	J [auth K]	142	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10 Go to UniProtKB: P0AA10
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UniProt Group	P0AA10
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	K [auth L]	123	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3 Go to UniProtKB: P0ADY3
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UniProt Group	P0ADY3
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	L [auth M]	144	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413 Go to UniProtKB: P02413
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UniProt Group	P02413
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	M [auth N]	136	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Explore P0ADY7 Go to UniProtKB: P0ADY7
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UniProt Group	P0ADY7
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	N [auth O]	127	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44 Go to UniProtKB: P0AG44
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UniProt Group	P0AG44
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	O [auth P]	117	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018 Go to UniProtKB: P0C018
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UniProt Group	P0C018
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	P [auth Q]	115	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6 Go to UniProtKB: P0A7K6
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7K6
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	Q [auth R]	118	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3 Go to UniProtKB: P0A7L3
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7L3
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	R [auth S]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48 Go to UniProtKB: P0AG48
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AG48
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	S [auth T]	110	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175 Go to UniProtKB: P61175
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61175
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	T [auth U]	100	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0 Go to UniProtKB: P0ADZ0
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ADZ0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	U [auth V]	104	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624 Go to UniProtKB: P60624
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60624
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	V [auth W]	94	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919 Go to UniProtKB: P68919
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UniProt Group	P68919
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	W [auth X]	85	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8 Go to UniProtKB: P0A7L8
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UniProt Group	P0A7L8
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	X [auth Y]	78	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Explore P0A7M2 Go to UniProtKB: P0A7M2
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7M2
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	Y [auth Z]	63	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Explore P0A7M6 Go to UniProtKB: P0A7M6
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7M6
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	Z [auth 0]	59	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51 Go to UniProtKB: P0AG51
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AG51
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	AA [auth 1]	57	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4 Go to UniProtKB: P0A7N4
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UniProt Group	P0A7N4
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	BA [auth 2]	55	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Explore P0A7N9 Go to UniProtKB: P0A7N9
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UniProt Group	P0A7N9
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	CA [auth 3]	46	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5 Go to UniProtKB: P0A7P5
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7P5
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	DA [auth 4]	65	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1 Go to UniProtKB: P0A7Q1
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UniProt Group	P0A7Q1
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	EA [auth 5]	38	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Explore P0A7Q6 Go to UniProtKB: P0A7Q6
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UniProt Group	P0A7Q6
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-binding ATPase YchF	FA [auth y]	379	Escherichia coli	Mutation(s): 1 Gene Names: ychF
UniProt
Find proteins for P0ABU2 (Escherichia coli (strain K12)) Explore P0ABU2 Go to UniProtKB: P0ABU2
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABU2
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
23S rRNA	A	2,904	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 2
5S rRNA	B	118	Escherichia coli
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain GE [auth 5] MOL2 format, chain GE [auth 5] mmCIF format, chain GE [auth 5]	GE [auth 5]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain GE [auth 5] Interactions & Density Focus chain GE [auth 5]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BC [auth A] SDF format, chain BE [auth B] SDF format, chain CB [auth A] SDF format, chain CD [auth A] SDF format, chain CE [auth B] SDF format, chain DB [auth A] SDF format, chain DD [auth A] SDF format, chain EB [auth A] SDF format, chain FD [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth A] SDF format, chain IB [auth A] SDF format, chain ID [auth A] SDF format, chain KA [auth A] SDF format, chain KD [auth A] SDF format, chain LA [auth A] SDF format, chain MB [auth A] SDF format, chain ND [auth A] SDF format, chain PB [auth A] SDF format, chain QC [auth A] SDF format, chain SB [auth A] SDF format, chain SD [auth A] SDF format, chain TB [auth A] SDF format, chain TD [auth A] SDF format, chain UA [auth A] SDF format, chain UC [auth A] SDF format, chain VA [auth A] SDF format, chain VC [auth A] SDF format, chain WA [auth A] SDF format, chain WD [auth A] SDF format, chain XB [auth A] SDF format, chain XD [auth A] SDF format, chain ZA [auth A] SDF format, chain ZD [auth A] SDF format, chain ZC [auth A] SDF format, chain ZB [auth A] SDF format, chain YD [auth A] SDF format, chain YC [auth A] SDF format, chain YB [auth A] SDF format, chain YA [auth A] SDF format, chain XC [auth A] SDF format, chain XA [auth A] SDF format, chain WC [auth A] SDF format, chain WB [auth A] SDF format, chain VD [auth A] SDF format, chain VB [auth A] SDF format, chain UD [auth A] SDF format, chain UB [auth A] SDF format, chain TC [auth A] SDF format, chain TA [auth A] SDF format, chain SC [auth A] SDF format, chain SA [auth A] SDF format, chain RD [auth A] SDF format, chain RC [auth A] SDF format, chain RB [auth A] SDF format, chain RA [auth A] SDF format, chain QD [auth A] SDF format, chain QB [auth A] SDF format, chain QA [auth A] SDF format, chain PD [auth A] SDF format, chain PC [auth A] SDF format, chain PA [auth A] SDF format, chain OD [auth A] SDF format, chain OC [auth A] SDF format, chain OB [auth A] SDF format, chain OA [auth A] SDF format, chain NC [auth A] SDF format, chain NB [auth A] SDF format, chain NA [auth A] SDF format, chain MD [auth A] SDF format, chain MC [auth A] SDF format, chain MA [auth A] SDF format, chain LD [auth A] SDF format, chain LC [auth A] SDF format, chain LB [auth A] SDF format, chain KC [auth A] SDF format, chain KB [auth A] SDF format, chain JD [auth A] SDF format, chain JC [auth A] SDF format, chain JB [auth A] SDF format, chain JA [auth A] SDF format, chain IC [auth A] SDF format, chain IA [auth A] SDF format, chain HD [auth A] SDF format, chain HC [auth A] SDF format, chain HB [auth A] SDF format, chain HA [auth A] SDF format, chain GD [auth A] SDF format, chain GC [auth A] SDF format, chain FE [auth D] SDF format, chain FC [auth A] SDF format, chain FB [auth A] SDF format, chain EE [auth B] SDF format, chain ED [auth A] SDF format, chain EC [auth A] SDF format, chain DE [auth B] SDF format, chain DC [auth A] SDF format, chain CC [auth A] SDF format, chain BD [auth A] SDF format, chain BB [auth A] SDF format, chain AE [auth A] SDF format, chain AD [auth A] SDF format, chain AC [auth A] SDF format, chain AB [auth A] MOL2 format, chain BC [auth A] MOL2 format, chain BE [auth B] MOL2 format, chain CB [auth A] MOL2 format, chain CD [auth A] MOL2 format, chain CE [auth B] MOL2 format, chain DB [auth A] MOL2 format, chain DD [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain FD [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain ID [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain KD [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain ND [auth A] MOL2 format, chain PB [auth A] MOL2 format, chain QC [auth A] MOL2 format, chain SB [auth A] MOL2 format, chain SD [auth A] MOL2 format, chain TB [auth A] MOL2 format, chain TD [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain UC [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain VC [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain WD [auth A] MOL2 format, chain XB [auth A] MOL2 format, chain XD [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain ZD [auth A] MOL2 format, chain ZC [auth A] MOL2 format, chain ZB [auth A] MOL2 format, chain YD [auth A] MOL2 format, chain YC [auth A] MOL2 format, chain YB [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain XC [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain WC [auth A] MOL2 format, chain WB [auth A] MOL2 format, chain VD [auth A] MOL2 format, chain VB [auth A] MOL2 format, chain UD [auth A] MOL2 format, chain UB [auth A] MOL2 format, chain TC [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain SC [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain RD [auth A] MOL2 format, chain RC [auth A] MOL2 format, chain RB [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain QD [auth A] MOL2 format, chain QB [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain PD [auth A] MOL2 format, chain PC [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain OD [auth A] MOL2 format, chain OC [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain NC [auth A] MOL2 format, chain NB [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain MD [auth A] MOL2 format, chain MC [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LD [auth A] MOL2 format, chain LC [auth A] MOL2 format, chain LB [auth A] MOL2 format, chain KC [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain JD [auth A] MOL2 format, chain JC [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain IC [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain HD [auth A] MOL2 format, chain HC [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain GD [auth A] MOL2 format, chain GC [auth A] MOL2 format, chain FE [auth D] MOL2 format, chain FC [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain EE [auth B] MOL2 format, chain ED [auth A] MOL2 format, chain EC [auth A] MOL2 format, chain DE [auth B] MOL2 format, chain DC [auth A] MOL2 format, chain CC [auth A] MOL2 format, chain BD [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain AE [auth A] MOL2 format, chain AD [auth A] MOL2 format, chain AC [auth A] MOL2 format, chain AB [auth A] mmCIF format, chain BC [auth A] mmCIF format, chain BE [auth B] mmCIF format, chain CB [auth A] mmCIF format, chain CD [auth A] mmCIF format, chain CE [auth B] mmCIF format, chain DB [auth A] mmCIF format, chain DD [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain FD [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth A] mmCIF format, chain IB [auth A] mmCIF format, chain ID [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain KD [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MB [auth A] mmCIF format, chain ND [auth A] mmCIF format, chain PB [auth A] mmCIF format, chain QC [auth A] mmCIF format, chain SB [auth A] mmCIF format, chain SD [auth A] mmCIF format, chain TB [auth A] mmCIF format, chain TD [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain UC [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain VC [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain WD [auth A] mmCIF format, chain XB [auth A] mmCIF format, chain XD [auth A] mmCIF format, chain ZA [auth A] mmCIF format, chain ZD [auth A] mmCIF format, chain ZC [auth A] mmCIF format, chain ZB [auth A] mmCIF format, chain YD [auth A] mmCIF format, chain YC [auth A] mmCIF format, chain YB [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain XC [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain WC [auth A] mmCIF format, chain WB [auth A] mmCIF format, chain VD [auth A] mmCIF format, chain VB [auth A] mmCIF format, chain UD [auth A] mmCIF format, chain UB [auth A] mmCIF format, chain TC [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain SC [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain RD [auth A] mmCIF format, chain RC [auth A] mmCIF format, chain RB [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain QD [auth A] mmCIF format, chain QB [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain PD [auth A] mmCIF format, chain PC [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain OD [auth A] mmCIF format, chain OC [auth A] mmCIF format, chain OB [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain NC [auth A] mmCIF format, chain NB [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain MD [auth A] mmCIF format, chain MC [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LD [auth A] mmCIF format, chain LC [auth A] mmCIF format, chain LB [auth A] mmCIF format, chain KC [auth A] mmCIF format, chain KB [auth A] mmCIF format, chain JD [auth A] mmCIF format, chain JC [auth A] mmCIF format, chain JB [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain IC [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain HD [auth A] mmCIF format, chain HC [auth A] mmCIF format, chain HB [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain GD [auth A] mmCIF format, chain GC [auth A] mmCIF format, chain FE [auth D] mmCIF format, chain FC [auth A] mmCIF format, chain FB [auth A] mmCIF format, chain EE [auth B] mmCIF format, chain ED [auth A] mmCIF format, chain EC [auth A] mmCIF format, chain DE [auth B] mmCIF format, chain DC [auth A] mmCIF format, chain CC [auth A] mmCIF format, chain BD [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain AE [auth A] mmCIF format, chain AD [auth A] mmCIF format, chain AC [auth A] mmCIF format, chain AB [auth A]	AB [auth A] AC [auth A] AD [auth A] AE [auth A] BB [auth A] AB [auth A], AC [auth A], AD [auth A], AE [auth A], BB [auth A], BC [auth A], BD [auth A], BE [auth B], CB [auth A], CC [auth A], CD [auth A], CE [auth B], DB [auth A], DC [auth A], DD [auth A], DE [auth B], EB [auth A], EC [auth A], ED [auth A], EE [auth B], FB [auth A], FC [auth A], FD [auth A], FE [auth D], GA [auth A], GB [auth A], GC [auth A], GD [auth A], HA [auth A], HB [auth A], HC [auth A], HD [auth A], IA [auth A], IB [auth A], IC [auth A], ID [auth A], JA [auth A], JB [auth A], JC [auth A], JD [auth A], KA [auth A], KB [auth A], KC [auth A], KD [auth A], LA [auth A], LB [auth A], LC [auth A], LD [auth A], MA [auth A], MB [auth A], MC [auth A], MD [auth A], NA [auth A], NB [auth A], NC [auth A], ND [auth A], OA [auth A], OB [auth A], OC [auth A], OD [auth A], PA [auth A], PB [auth A], PC [auth A], PD [auth A], QA [auth A], QB [auth A], QC [auth A], QD [auth A], RA [auth A], RB [auth A], RC [auth A], RD [auth A], SA [auth A], SB [auth A], SC [auth A], SD [auth A], TA [auth A], TB [auth A], TC [auth A], TD [auth A], UA [auth A], UB [auth A], UC [auth A], UD [auth A], VA [auth A], VB [auth A], VC [auth A], VD [auth A], WA [auth A], WB [auth A], WC [auth A], WD [auth A], XA [auth A], XB [auth A], XC [auth A], XD [auth A], YA [auth A], YB [auth A], YC [auth A], YD [auth A], ZA [auth A], ZB [auth A], ZC [auth A], ZD [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth A] Focus chain AC [auth A] Focus chain AD [auth A] Focus chain AE [auth A] Focus chain BB [auth A] Focus chain BC [auth A] Focus chain BD [auth A] Focus chain BE [auth B] Focus chain CB [auth A] Focus chain CC [auth A] Focus chain CD [auth A] Focus chain CE [auth B] Focus chain DB [auth A] Focus chain DC [auth A] Focus chain DD [auth A] Focus chain DE [auth B] Focus chain EB [auth A] Focus chain EC [auth A] Focus chain ED [auth A] Focus chain EE [auth B] Focus chain FB [auth A] Focus chain FC [auth A] Focus chain FD [auth A] Focus chain FE [auth D] Focus chain GA [auth A] Focus chain GB [auth A] Focus chain GC [auth A] Focus chain GD [auth A] Focus chain HA [auth A] Focus chain HB [auth A] Focus chain HC [auth A] Focus chain HD [auth A] Focus chain IA [auth A] Focus chain IB [auth A] Focus chain IC [auth A] Focus chain ID [auth A] Focus chain JA [auth A] Focus chain JB [auth A] Focus chain JC [auth A] Focus chain JD [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain KC [auth A] Focus chain KD [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LC [auth A] Focus chain LD [auth A] Focus chain MA [auth A] Focus chain MB [auth A] Focus chain MC [auth A] Focus chain MD [auth A] Focus chain NA [auth A] Focus chain NB [auth A] Focus chain NC [auth A] Focus chain ND [auth A] Focus chain OA [auth A] Focus chain OB [auth A] Focus chain OC [auth A] Focus chain OD [auth A] Focus chain PA [auth A] Focus chain PB [auth A] Focus chain PC [auth A] Focus chain PD [auth A] Focus chain QA [auth A] Focus chain QB [auth A] Focus chain QC [auth A] Focus chain QD [auth A] Focus chain RA [auth A] Focus chain RB [auth A] Focus chain RC [auth A] Focus chain RD [auth A] Focus chain SA [auth A] Focus chain SB [auth A] Focus chain SC [auth A] Focus chain SD [auth A] Focus chain TA [auth A] Focus chain TB [auth A] Focus chain TC [auth A] Focus chain TD [auth A] Focus chain UA [auth A] Focus chain UB [auth A] Focus chain UC [auth A] Focus chain UD [auth A] Focus chain VA [auth A] Focus chain VB [auth A] Focus chain VC [auth A] Focus chain VD [auth A] Focus chain WA [auth A] Focus chain WB [auth A] Focus chain WC [auth A] Focus chain WD [auth A] Focus chain XA [auth A] Focus chain XB [auth A] Focus chain XC [auth A] Focus chain XD [auth A] Focus chain YA [auth A] Focus chain YB [auth A] Focus chain YC [auth A] Focus chain YD [auth A] Focus chain ZA [auth A] Focus chain ZB [auth A] Focus chain ZC [auth A] Focus chain ZD [auth A] Interactions & Density Focus chain AB [auth A] Focus chain AC [auth A] Focus chain AD [auth A] Focus chain AE [auth A] Focus chain BB [auth A] Focus chain BC [auth A] Focus chain BD [auth A] Focus chain BE [auth B] Focus chain CB [auth A] Focus chain CC [auth A] Focus chain CD [auth A] Focus chain CE [auth B] Focus chain DB [auth A] Focus chain DC [auth A] Focus chain DD [auth A] Focus chain DE [auth B] Focus chain EB [auth A] Focus chain EC [auth A] Focus chain ED [auth A] Focus chain EE [auth B] Focus chain FB [auth A] Focus chain FC [auth A] Focus chain FD [auth A] Focus chain FE [auth D] Focus chain GA [auth A] Focus chain GB [auth A] Focus chain GC [auth A] Focus chain GD [auth A] Focus chain HA [auth A] Focus chain HB [auth A] Focus chain HC [auth A] Focus chain HD [auth A] Focus chain IA [auth A] Focus chain IB [auth A] Focus chain IC [auth A] Focus chain ID [auth A] Focus chain JA [auth A] Focus chain JB [auth A] Focus chain JC [auth A] Focus chain JD [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain KC [auth A] Focus chain KD [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LC [auth A] Focus chain LD [auth A] Focus chain MA [auth A] Focus chain MB [auth A] Focus chain MC [auth A] Focus chain MD [auth A] Focus chain NA [auth A] Focus chain NB [auth A] Focus chain NC [auth A] Focus chain ND [auth A] Focus chain OA [auth A] Focus chain OB [auth A] Focus chain OC [auth A] Focus chain OD [auth A] Focus chain PA [auth A] Focus chain PB [auth A] Focus chain PC [auth A] Focus chain PD [auth A] Focus chain QA [auth A] Focus chain QB [auth A] Focus chain QC [auth A] Focus chain QD [auth A] Focus chain RA [auth A] Focus chain RB [auth A] Focus chain RC [auth A] Focus chain RD [auth A] Focus chain SA [auth A] Focus chain SB [auth A] Focus chain SC [auth A] Focus chain SD [auth A] Focus chain TA [auth A] Focus chain TB [auth A] Focus chain TC [auth A] Focus chain TD [auth A] Focus chain UA [auth A] Focus chain UB [auth A] Focus chain UC [auth A] Focus chain UD [auth A] Focus chain VA [auth A] Focus chain VB [auth A] Focus chain VC [auth A] Focus chain VD [auth A] Focus chain WA [auth A] Focus chain WB [auth A] Focus chain WC [auth A] Focus chain WD [auth A] Focus chain XA [auth A] Focus chain XB [auth A] Focus chain XC [auth A] Focus chain XD [auth A] Focus chain YA [auth A] Focus chain YB [auth A] Focus chain YC [auth A] Focus chain YD [auth A] Focus chain ZA [auth A] Focus chain ZB [auth A] Focus chain ZC [auth A] Focus chain ZD [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Yu, T.

Li, X.

Zeng, F.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171200
Guangdong Basic and Applied Basic Research Foundation	China	2021A1515010805
Shenzhen Science and Technology Program	China	JCYJ20220530115210023

Revision History (Full details and data files)

Version 1.0: 2024-08-28
Type: Initial release
Version 1.1: 2025-06-25
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

8W51 | pdb_00008w51

Structure of YchF(H114A) on E.coli 50S ribosomal subunit

Literature

Structure basis of translation regulation by YchF bound to ribosome

Biological Assembly 1

Macromolecules

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