7VPX

The cryo-EM structure of the human pre-A complex

• PDB DOI: https://doi.org/10.2210/pdb7VPX/pdb
• NAKB: 7VPX
• EM Map EMD-32074: EMDB EMDataResource

• Classification: SPLICING
• Organism(s): Homo sapiens, unidentified adenovirus
• Mutation(s): No 


• Deposited: 2021-10-18 Released: 2023-05-03 
• Deposition Author(s): Zhang, X., Zhan, X., Shi, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism for Branch Site Recognition and Proofreading During Prespliceosome Assembly

Zhang, X., Zhan, X., Shi, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 31-mer - A2B2C2D2E2F2G2H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 31-mer - A14B2C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - D2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - E2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - F2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - G2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 1,405.82 kDa 
• Atom Count: 43,240 
• Modelled Residue Count: 5,930 
• Deposited Residue Count: 11,410 
• Unique protein chains: 24
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3A subunit 2	A [auth B]	464	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15428 (Homo sapiens) Explore Q15428  Go to UniProtKB:  Q15428
PHAROS:  Q15428 GTEx:  ENSG00000104897

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 1	B [auth D]	639	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15637 (Homo sapiens) Explore Q15637  Go to UniProtKB:  Q15637
PHAROS:  Q15637 GTEx:  ENSG00000168066

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaJ homolog subfamily C member 8	C [auth J]	253	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75937 (Homo sapiens) Explore O75937  Go to UniProtKB:  O75937
PHAROS:  O75937 GTEx:  ENSG00000126698

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 1	E [auth 1]	1,304	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75533 (Homo sapiens) Explore O75533  Go to UniProtKB:  O75533
PHAROS:  O75533 GTEx:  ENSG00000115524

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 2	F [auth 2]	895	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13435 (Homo sapiens) Explore Q13435  Go to UniProtKB:  Q13435
PHAROS:  Q13435 GTEx:  ENSG00000087365

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 3	G [auth 3]	1,217	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15393 (Homo sapiens) Explore Q15393  Go to UniProtKB:  Q15393
PHAROS:  Q15393 GTEx:  ENSG00000189091

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 4	H [auth 4]	424	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15427 (Homo sapiens) Explore Q15427  Go to UniProtKB:  Q15427
PHAROS:  Q15427 GTEx:  ENSG00000143368

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 5	I [auth 5]	86	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BWJ5 (Homo sapiens) Explore Q9BWJ5  Go to UniProtKB:  Q9BWJ5
PHAROS:  Q9BWJ5 GTEx:  ENSG00000169976

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3A subunit 1	J [auth A]	793	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15459 (Homo sapiens) Explore Q15459  Go to UniProtKB:  Q15459
PHAROS:  Q15459 GTEx:  ENSG00000099995

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3A subunit 3	K [auth C]	501	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q12874 (Homo sapiens) Explore Q12874  Go to UniProtKB:  Q12874
PHAROS:  Q12874 GTEx:  ENSG00000183431

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX46	L [auth E]	1,031	Homo sapiens	Mutation(s): 0  EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L014 (Homo sapiens) Explore Q7L014  Go to UniProtKB:  Q7L014
PHAROS:  Q7L014 GTEx:  ENSG00000145833

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
U2 small nuclear ribonucleoprotein A'	M [auth F]	255	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09661 (Homo sapiens) Explore P09661  Go to UniProtKB:  P09661
GTEx:  ENSG00000131876

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
U2 small nuclear ribonucleoprotein B''	N [auth G]	225	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P08579 (Homo sapiens) Explore P08579  Go to UniProtKB:  P08579
PHAROS:  P08579 GTEx:  ENSG00000125870

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein Sm D2	FA [auth i], O [auth a]	118	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62316 (Homo sapiens) Explore P62316  Go to UniProtKB:  P62316
PHAROS:  P62316 GTEx:  ENSG00000125743

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein F	P [auth b], Z [auth m]	86	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62306 (Homo sapiens) Explore P62306  Go to UniProtKB:  P62306
PHAROS:  P62306 GTEx:  ENSG00000139343

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein E	EA [auth l], Q [auth c]	92	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62304 (Homo sapiens) Explore P62304  Go to UniProtKB:  P62304
PHAROS:  P62304 GTEx:  ENSG00000182004

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein G	DA [auth n], R [auth d]	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62308 (Homo sapiens) Explore P62308  Go to UniProtKB:  P62308
PHAROS:  P62308 GTEx:  ENSG00000143977

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein Sm D3	HA [auth j], S [auth e]	126	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62318 (Homo sapiens) Explore P62318  Go to UniProtKB:  P62318
PHAROS:  P62318 GTEx:  ENSG00000100028

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein-associated proteins B and B'	BA [auth k], T [auth f]	240	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P14678 (Homo sapiens) Explore P14678  Go to UniProtKB:  P14678
PHAROS:  P14678 GTEx:  ENSG00000125835

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein Sm D1	AA [auth h], U [auth g]	119	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens) Explore P62314  Go to UniProtKB:  P62314
PHAROS:  P62314 GTEx:  ENSG00000167088

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein 70 kDa	Y [auth O]	437	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P08621 (Homo sapiens) Explore P08621  Go to UniProtKB:  P08621
PHAROS:  P08621 GTEx:  ENSG00000104852

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	CA [auth M]	282	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012 GTEx:  ENSG00000077312

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein C	GA [auth N]	159	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09234 (Homo sapiens) Explore P09234  Go to UniProtKB:  P09234
PHAROS:  P09234 GTEx:  ENSG00000124562

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger-like domain-containing protein 5A	IA [auth 6]	110	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q7RTV0 (Homo sapiens) Explore Q7RTV0  Go to UniProtKB:  Q7RTV0
PHAROS:  Q7RTV0 GTEx:  ENSG00000100410

Entity ID: 4
Molecule	Chains	Length	Organism	Image
U2 snRNA	D [auth H]	188	Homo sapiens

Entity ID: 22
Molecule	Chains	Length	Organism	Image
pre-mRNA	V [auth I]	259	unidentified adenovirus

Entity ID: 23
Molecule	Chains	Length	Organism	Image
5SS	W [auth K]	10	unidentified adenovirus

Entity ID: 24
Molecule	Chains	Length	Organism	Image
U1 snRNA	X [auth L]	164	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SJT (Subject of Investigation/LOI)	PA [auth 6]	spliceostatin A (form II) C28 H45 N O8 KFBJURVXOOMXKK-GSHHMAPISA-N
ZN	JA [auth B], KA [auth C], LA [auth N], MA [auth 6], NA [auth 6], OA [auth 6]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): Zhang, X., Zhan, X., Shi, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release