9NRD | pdb_00009nrd

CCT G beta 5 G257E complex state 2

PDB DOI: https://doi.org/10.2210/pdb9NRD/pdb
EM Map EMD-49729: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-03-14 Released: 2026-04-01
Deposition Author(s): Mack, D.C., Shen, P.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Disease-causing mutations in the G protein beta 5 beta-propeller disrupt its Chaperonin-mediated Folding Trajectory

Sass, M., Mack, D.C., Shen, P.S., Willardson, B.M.

To be published.

Macromolecule Content

Total Structure Weight: 1,004.15 kDa
Atom Count: 65,279
Modeled Residue Count: 8,481
Deposited Residue Count: 9,117
Unique protein chains: 9

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein subunit beta-5	A [auth N]	441	Homo sapiens	Mutation(s): 1 Gene Names: GNB5
UniProt & NIH Common Fund Data Resources
Find proteins for O14775 (Homo sapiens) Explore O14775 Go to UniProtKB: O14775
PHAROS: O14775 GTEx: ENSG00000069966
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14775
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit alpha	B [auth A], J [auth a]	556	Homo sapiens	Mutation(s): 0 EC: 3.6.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17987
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit beta	C [auth B], K [auth b]	535	Homo sapiens	Mutation(s): 0 EC: 3.6.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78371
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit delta	D, L [auth d]	539	Homo sapiens	Mutation(s): 0 EC: 3.6.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50991
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit epsilon	E, M [auth e]	541	Homo sapiens	Mutation(s): 0 EC: 3.6.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48643
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit gamma	F [auth G], N [auth g]	545	Homo sapiens	Mutation(s): 0 EC: 3.6.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49368
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit eta	G [auth H], O [auth h]	543	Homo sapiens	Mutation(s): 0 EC: 3.6.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99832
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit theta	H [auth Q], P [auth q]	548	Homo sapiens	Mutation(s): 0 EC: 3.6.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50990
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit zeta	I [auth Z], Q [auth z]	531	Homo sapiens	Mutation(s): 0 EC: 3.6.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40227
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-01

Deposition Author(s):

Mack, D.C.

Shen, P.S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM133772
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	R01 EY012287
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	R01 EY036925

Revision History (Full details and data files)

Version 1.0: 2026-04-01
Type: Initial release

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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.

9NRD | pdb_00009nrd

CCT G beta 5 G257E complex state 2

Literature

Disease-causing mutations in the G protein beta 5 beta-propeller disrupt its Chaperonin-mediated Folding Trajectory

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)