8I1U

Human TRiC-PhLP2A complex in the closed state

PDB DOI: https://doi.org/10.2210/pdb8I1U/pdb
EM Map EMD-35122: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): No

Deposited: 2023-01-13 Released: 2024-01-31
Deposition Author(s): Roh, S.H., Park, J., Kim, H., Lim, S.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.24 Å
Aggregation State: 2D ARRAY
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Human TRiC-PhLP2A complex in the closed state

Roh, S.H., Park, J., Lim, S., Kim, H.

To be published.

Macromolecule Content

Total Structure Weight: 1,011.04 kDa
Atom Count: 67,629
Modelled Residue Count: 8,763
Deposited Residue Count: 9,154
Unique protein chains: 9

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit alpha	A, I	556	Homo sapiens	Mutation(s): 0 Gene Names: TCP1, CCT1, CCTA
UniProt & NIH Common Fund Data Resources
Find proteins for P17987 (Homo sapiens) Explore P17987 Go to UniProtKB: P17987
PHAROS: P17987 GTEx: ENSG00000120438
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17987
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit beta	B, J	535	Homo sapiens	Mutation(s): 0 Gene Names: CCT2, 99D8.1, CCTB
UniProt & NIH Common Fund Data Resources
Find proteins for P78371 (Homo sapiens) Explore P78371 Go to UniProtKB: P78371
PHAROS: P78371 GTEx: ENSG00000166226
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P78371
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit gamma	C, K	545	Homo sapiens	Mutation(s): 0 Gene Names: CCT3, CCTG, TRIC5
UniProt & NIH Common Fund Data Resources
Find proteins for P49368 (Homo sapiens) Explore P49368 Go to UniProtKB: P49368
PHAROS: P49368 GTEx: ENSG00000163468
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49368
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit delta	D, L	539	Homo sapiens	Mutation(s): 0 Gene Names: CCT4, CCTD, SRB
UniProt & NIH Common Fund Data Resources
Find proteins for P50991 (Homo sapiens) Explore P50991 Go to UniProtKB: P50991
PHAROS: P50991 GTEx: ENSG00000115484
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50991
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit epsilon	E, M	541	Homo sapiens	Mutation(s): 0 Gene Names: CCT5, CCTE, KIAA0098
UniProt & NIH Common Fund Data Resources
Find proteins for P48643 (Homo sapiens) Explore P48643 Go to UniProtKB: P48643
PHAROS: P48643 GTEx: ENSG00000150753
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48643
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit zeta	F, N	531	Homo sapiens	Mutation(s): 0 Gene Names: CCT6A, CCT6, CCTZ
UniProt & NIH Common Fund Data Resources
Find proteins for P40227 (Homo sapiens) Explore P40227 Go to UniProtKB: P40227
PHAROS: P40227 GTEx: ENSG00000146731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40227
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit eta	G, O	543	Homo sapiens	Mutation(s): 0 Gene Names: CCT7, CCTH, NIP7-1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99832 (Homo sapiens) Explore Q99832 Go to UniProtKB: Q99832
PHAROS: Q99832 GTEx: ENSG00000135624
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99832
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit theta	H, P	548	Homo sapiens	Mutation(s): 0 Gene Names: CCT8, C21orf112, CCTQ
UniProt & NIH Common Fund Data Resources
Find proteins for P50990 (Homo sapiens) Explore P50990 Go to UniProtKB: P50990
PHAROS: P50990 GTEx: ENSG00000156261
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50990
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosducin-like protein 3	Q, R	239	Homo sapiens	Mutation(s): 0 Gene Names: PDCL3, PhLP2A, VIAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2J4 (Homo sapiens) Explore Q9H2J4 Go to UniProtKB: Q9H2J4
GTEx: ENSG00000115539
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H2J4
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CB [auth M] SDF format, chain EA [auth E] SDF format, chain FB [auth N] SDF format, chain HA [auth F] SDF format, chain IB [auth O] SDF format, chain KA [auth G] SDF format, chain LB [auth P] SDF format, chain NA [auth H] SDF format, chain QA [auth I] SDF format, chain S [auth A] SDF format, chain TA [auth J] SDF format, chain V [auth B] SDF format, chain WA [auth K] SDF format, chain Y [auth C] SDF format, chain ZA [auth L] MOL2 format, chain BA [auth D] MOL2 format, chain CB [auth M] MOL2 format, chain EA [auth E] MOL2 format, chain FB [auth N] MOL2 format, chain HA [auth F] MOL2 format, chain IB [auth O] MOL2 format, chain KA [auth G] MOL2 format, chain LB [auth P] MOL2 format, chain NA [auth H] MOL2 format, chain QA [auth I] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth J] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth K] MOL2 format, chain Y [auth C] MOL2 format, chain ZA [auth L]	BA [auth D] CB [auth M] EA [auth E] FB [auth N] HA [auth F] BA [auth D], CB [auth M], EA [auth E], FB [auth N], HA [auth F], IB [auth O], KA [auth G], LB [auth P], NA [auth H], QA [auth I], S [auth A], TA [auth J], V [auth B], WA [auth K], Y [auth C], ZA [auth L]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth D] Focus chain CB [auth M] Focus chain EA [auth E] Focus chain FB [auth N] Focus chain HA [auth F] Focus chain IB [auth O] Focus chain KA [auth G] Focus chain LB [auth P] Focus chain NA [auth H] Focus chain QA [auth I] Focus chain S [auth A] Focus chain TA [auth J] Focus chain V [auth B] Focus chain WA [auth K] Focus chain Y [auth C] Focus chain ZA [auth L] Interactions & Density Focus chain BA [auth D] Focus chain CB [auth M] Focus chain EA [auth E] Focus chain FB [auth N] Focus chain HA [auth F] Focus chain IB [auth O] Focus chain KA [auth G] Focus chain LB [auth P] Focus chain NA [auth H] Focus chain QA [auth I] Focus chain S [auth A] Focus chain TA [auth J] Focus chain V [auth B] Focus chain WA [auth K] Focus chain Y [auth C] Focus chain ZA [auth L]
AF3 (Subject of Investigation/LOI) Query on AF3 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth L] SDF format, chain DA [auth D] SDF format, chain EB [auth M] SDF format, chain GA [auth E] SDF format, chain HB [auth N] SDF format, chain JA [auth F] SDF format, chain KB [auth O] SDF format, chain MA [auth G] SDF format, chain NB [auth P] SDF format, chain PA [auth H] SDF format, chain SA [auth I] SDF format, chain U [auth A] SDF format, chain VA [auth J] SDF format, chain X [auth B] SDF format, chain YA [auth K] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth L] MOL2 format, chain DA [auth D] MOL2 format, chain EB [auth M] MOL2 format, chain GA [auth E] MOL2 format, chain HB [auth N] MOL2 format, chain JA [auth F] MOL2 format, chain KB [auth O] MOL2 format, chain MA [auth G] MOL2 format, chain NB [auth P] MOL2 format, chain PA [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth J] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth K]	AA [auth C] BB [auth L] DA [auth D] EB [auth M] GA [auth E] AA [auth C], BB [auth L], DA [auth D], EB [auth M], GA [auth E], HB [auth N], JA [auth F], KB [auth O], MA [auth G], NB [auth P], PA [auth H], SA [auth I], U [auth A], VA [auth J], X [auth B], YA [auth K]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain BB [auth L] Focus chain DA [auth D] Focus chain EB [auth M] Focus chain GA [auth E] Focus chain HB [auth N] Focus chain JA [auth F] Focus chain KB [auth O] Focus chain MA [auth G] Focus chain NB [auth P] Focus chain PA [auth H] Focus chain SA [auth I] Focus chain U [auth A] Focus chain VA [auth J] Focus chain X [auth B] Focus chain YA [auth K] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth L] Focus chain DA [auth D] Focus chain EB [auth M] Focus chain GA [auth E] Focus chain HB [auth N] Focus chain JA [auth F] Focus chain KB [auth O] Focus chain MA [auth G] Focus chain NB [auth P] Focus chain PA [auth H] Focus chain SA [auth I] Focus chain U [auth A] Focus chain VA [auth J] Focus chain X [auth B] Focus chain YA [auth K]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain CA [auth D] SDF format, chain DB [auth M] SDF format, chain FA [auth E] SDF format, chain GB [auth N] SDF format, chain IA [auth F] SDF format, chain JB [auth O] SDF format, chain LA [auth G] SDF format, chain MB [auth P] SDF format, chain OA [auth H] SDF format, chain RA [auth I] SDF format, chain T [auth A] SDF format, chain UA [auth J] SDF format, chain W [auth B] SDF format, chain XA [auth K] SDF format, chain Z [auth C] MOL2 format, chain AB [auth L] MOL2 format, chain CA [auth D] MOL2 format, chain DB [auth M] MOL2 format, chain FA [auth E] MOL2 format, chain GB [auth N] MOL2 format, chain IA [auth F] MOL2 format, chain JB [auth O] MOL2 format, chain LA [auth G] MOL2 format, chain MB [auth P] MOL2 format, chain OA [auth H] MOL2 format, chain RA [auth I] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth J] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth K] MOL2 format, chain Z [auth C]	AB [auth L] CA [auth D] DB [auth M] FA [auth E] GB [auth N] AB [auth L], CA [auth D], DB [auth M], FA [auth E], GB [auth N], IA [auth F], JB [auth O], LA [auth G], MB [auth P], OA [auth H], RA [auth I], T [auth A], UA [auth J], W [auth B], XA [auth K], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth L] Focus chain CA [auth D] Focus chain DB [auth M] Focus chain FA [auth E] Focus chain GB [auth N] Focus chain IA [auth F] Focus chain JB [auth O] Focus chain LA [auth G] Focus chain MB [auth P] Focus chain OA [auth H] Focus chain RA [auth I] Focus chain T [auth A] Focus chain UA [auth J] Focus chain W [auth B] Focus chain XA [auth K] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth L] Focus chain CA [auth D] Focus chain DB [auth M] Focus chain FA [auth E] Focus chain GB [auth N] Focus chain IA [auth F] Focus chain JB [auth O] Focus chain LA [auth G] Focus chain MB [auth P] Focus chain OA [auth H] Focus chain RA [auth I] Focus chain T [auth A] Focus chain UA [auth J] Focus chain W [auth B] Focus chain XA [auth K] Focus chain Z [auth C]