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

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14775
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17987
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P78371
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50991
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48643
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49368
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99832
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50990
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 AA [auth E] SDF format, chain BB [auth g] SDF format, chain DA [auth G] SDF format, chain EB [auth h] SDF format, chain GA [auth H] SDF format, chain HB [auth q] SDF format, chain JA [auth Q] SDF format, chain KB [auth z] SDF format, chain MA [auth Z] SDF format, chain PA [auth a] SDF format, chain R [auth A] SDF format, chain SA [auth b] SDF format, chain U [auth B] SDF format, chain VA [auth d] SDF format, chain X [auth D] SDF format, chain YA [auth e] MOL2 format, chain AA [auth E] MOL2 format, chain BB [auth g] MOL2 format, chain DA [auth G] MOL2 format, chain EB [auth h] MOL2 format, chain GA [auth H] MOL2 format, chain HB [auth q] MOL2 format, chain JA [auth Q] MOL2 format, chain KB [auth z] MOL2 format, chain MA [auth Z] MOL2 format, chain PA [auth a] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth b] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth d] MOL2 format, chain X [auth D] MOL2 format, chain YA [auth e] mmCIF format, chain AA [auth E] mmCIF format, chain BB [auth g] mmCIF format, chain DA [auth G] mmCIF format, chain EB [auth h] mmCIF format, chain GA [auth H] mmCIF format, chain HB [auth q] mmCIF format, chain JA [auth Q] mmCIF format, chain KB [auth z] mmCIF format, chain MA [auth Z] mmCIF format, chain PA [auth a] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth b] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth d] mmCIF format, chain X [auth D] mmCIF format, chain YA [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 AB [auth e] SDF format, chain CA [auth E] SDF format, chain DB [auth g] SDF format, chain FA [auth G] SDF format, chain GB [auth h] SDF format, chain IA [auth H] SDF format, chain JB [auth q] SDF format, chain LA [auth Q] SDF format, chain MB [auth z] SDF format, chain OA [auth Z] SDF format, chain RA [auth a] SDF format, chain T [auth A] SDF format, chain UA [auth b] SDF format, chain W [auth B] SDF format, chain XA [auth d] SDF format, chain Z [auth D] MOL2 format, chain AB [auth e] MOL2 format, chain CA [auth E] MOL2 format, chain DB [auth g] MOL2 format, chain FA [auth G] MOL2 format, chain GB [auth h] MOL2 format, chain IA [auth H] MOL2 format, chain JB [auth q] MOL2 format, chain LA [auth Q] MOL2 format, chain MB [auth z] MOL2 format, chain OA [auth Z] MOL2 format, chain RA [auth a] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth b] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth d] MOL2 format, chain Z [auth D] mmCIF format, chain AB [auth e] mmCIF format, chain CA [auth E] mmCIF format, chain DB [auth g] mmCIF format, chain FA [auth G] mmCIF format, chain GB [auth h] mmCIF format, chain IA [auth H] mmCIF format, chain JB [auth q] mmCIF format, chain LA [auth Q] mmCIF format, chain MB [auth z] mmCIF format, chain OA [auth Z] mmCIF format, chain RA [auth a] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth b] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth d] mmCIF format, chain Z [auth D]	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 BA [auth E] SDF format, chain CB [auth g] SDF format, chain EA [auth G] SDF format, chain FB [auth h] SDF format, chain HA [auth H] SDF format, chain IB [auth q] SDF format, chain KA [auth Q] SDF format, chain LB [auth z] SDF format, chain NA [auth Z] SDF format, chain QA [auth a] SDF format, chain S [auth A] SDF format, chain TA [auth b] SDF format, chain V [auth B] SDF format, chain WA [auth d] SDF format, chain Y [auth D] SDF format, chain ZA [auth e] MOL2 format, chain BA [auth E] MOL2 format, chain CB [auth g] MOL2 format, chain EA [auth G] MOL2 format, chain FB [auth h] MOL2 format, chain HA [auth H] MOL2 format, chain IB [auth q] MOL2 format, chain KA [auth Q] MOL2 format, chain LB [auth z] MOL2 format, chain NA [auth Z] MOL2 format, chain QA [auth a] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth b] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth d] MOL2 format, chain Y [auth D] MOL2 format, chain ZA [auth e] mmCIF format, chain BA [auth E] mmCIF format, chain CB [auth g] mmCIF format, chain EA [auth G] mmCIF format, chain FB [auth h] mmCIF format, chain HA [auth H] mmCIF format, chain IB [auth q] mmCIF format, chain KA [auth Q] mmCIF format, chain LB [auth z] mmCIF format, chain NA [auth Z] mmCIF format, chain QA [auth a] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth b] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth d] mmCIF format, chain Y [auth D] mmCIF format, chain ZA [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

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