8XL3 | pdb_00008xl3

Structure of human propionyl-CoA carboxylase at apo-state (PCC-Apo)

PDB DOI: https://doi.org/10.2210/pdb8XL3/pdb
EM Map EMD-38436: EMDB EMDataResource

Classification: LIGASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2023-12-25 Released: 2024-10-30
Deposition Author(s): Zhou, F.Y., Zhang, Y.Y., Zhou, Q., Hu, Q.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8XL3

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

Literature

Structural insights into human propionyl-CoA carboxylase (PCC) and 3-methylcrotonyl-CoA carboxylase (MCC)

Zhou, F., Zhang, Y., Zhu, Y., Zhou, Q., Shi, Y., Hu, Q.

(2024) Elife

DOI: https://doi.org/10.7554/elife.98885.2

Macromolecule Content

Total Structure Weight: 832.14 kDa
Atom Count: 54,204
Modeled Residue Count: 7,050
Deposited Residue Count: 7,602
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase alpha chain, mitochondrial	A, C, E, G, I A, C, E, G, I, K	728	Homo sapiens	Mutation(s): 0 EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05165 (Homo sapiens) Explore P05165 Go to UniProtKB: P05165
PHAROS: P05165 GTEx: ENSG00000175198
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05165
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain, mitochondrial	B, D, F, H, J B, D, F, H, J, L	539	Homo sapiens	Mutation(s): 0 EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05166 (Homo sapiens) Explore P05166 Go to UniProtKB: P05166
PHAROS: P05166 GTEx: ENSG00000114054
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTN (Subject of Investigation/LOI) Query on BTN Download:Ideal Coordinates CCD File SDF format, chain R [auth K] SDF format, chain Q [auth I] SDF format, chain P [auth G] SDF format, chain O [auth E] SDF format, chain N [auth C] SDF format, chain M [auth A] MOL2 format, chain R [auth K] MOL2 format, chain Q [auth I] MOL2 format, chain P [auth G] MOL2 format, chain O [auth E] MOL2 format, chain N [auth C] MOL2 format, chain M [auth A] mmCIF format, chain R [auth K] mmCIF format, chain Q [auth I] mmCIF format, chain P [auth G] mmCIF format, chain O [auth E] mmCIF format, chain N [auth C] mmCIF format, chain M [auth A]	M [auth A] N [auth C] O [auth E] P [auth G] Q [auth I] M [auth A], N [auth C], O [auth E], P [auth G], Q [auth I], R [auth K]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth E] Focus chain P [auth G] Focus chain Q [auth I] Focus chain R [auth K] Interactions & Density Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth E] Focus chain P [auth G] Focus chain Q [auth I] Focus chain R [auth K]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		Westlake Education Foundation No. 101256021901

Revision History (Full details and data files)

Version 1.0: 2024-10-30
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection

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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.