[English] 日本語
Yorodumi
- PDB-8zv0: Structure of G131R-hPCC BCCP-CT Conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zv0
TitleStructure of G131R-hPCC BCCP-CT Conformation
Components
  • (Propionyl-CoA carboxylase beta chain, ...) x 2
  • Propionyl-CoA carboxylase alpha chain, mitochondrial
KeywordsTRANSFERASE / BIOTIN / CARBOXYLASE
Function / homology
Function and homology information


short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / Mitochondrial protein degradation ...short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / Mitochondrial protein degradation / fatty acid metabolic process / mitochondrial matrix / enzyme binding / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain ...Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / BICARBONATE ION / BIOTIN / Propionyl-CoA carboxylase alpha chain, mitochondrial / Propionyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsNi, F. / Yan, H. / Wang, Q. / Ma, J.
Funding support China, 2items
OrganizationGrant numberCountry
Other government2021YFF1200400 China
Other government2018SHZDZX01 China
CitationJournal: Structure / Year: 2025
Title: Nanoscale conformational dynamics of human propionyl-CoA carboxylase.
Authors: Huifang Yan / Fengyun Ni / Qinghua Wang / Jianpeng Ma /
Abstract: Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic ...Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic disorder driven by toxic metabolite accumulation. Despite its therapeutic relevance, the structural basis of hPCC's catalytic function remains unresolved. Here, we present high-resolution cryo-EM structures of hPCC in four distinct states, unliganded, ADP-, AMPPNP-, and ATP-bound/substrate-bound, capturing the full trajectory of the biotin carboxyl carrier protein (BCCP) domain as it translocates between active sites. Our results reinforce the crucial role of nucleotide-gated B-lid subdomain in synchronizing catalysis through coupling with BCCP movement. Structural and biochemical analysis of 10 disease-associated variants reveals how mutations disrupt key domain interfaces and dynamic motions required for activity. These new insights define the mechanistic principles governing hPCC functions, establish a structural framework for understanding PCC-related disorders, and lay the groundwork for future efforts to engineer functional replacements or modulators for metabolic therapy.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Propionyl-CoA carboxylase alpha chain, mitochondrial
B: Propionyl-CoA carboxylase beta chain, mitochondrial
F: Propionyl-CoA carboxylase beta chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,4027
Polymers138,5653
Non-polymers8374
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Propionyl-CoA carboxylase alpha chain, mitochondrial / PCCase subunit alpha / Propanoyl-CoA:carbon dioxide ligase subunit alpha


Mass: 80161.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCCA / Production host: Homo sapiens (human) / References: UniProt: P05165, propionyl-CoA carboxylase

-
Propionyl-CoA carboxylase beta chain, ... , 2 types, 2 molecules BF

#2: Protein Propionyl-CoA carboxylase beta chain, mitochondrial / PCCase subunit beta / Propanoyl-CoA:carbon dioxide ligase subunit beta


Mass: 27095.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCCB / Production host: Homo sapiens (human) / References: UniProt: P05166, propionyl-CoA carboxylase
#3: Protein Propionyl-CoA carboxylase beta chain, mitochondrial / PCCase subunit beta / Propanoyl-CoA:carbon dioxide ligase subunit beta


Mass: 31307.631 Da / Num. of mol.: 1 / Mutation: G131R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCCB / Production host: Homo sapiens (human) / References: UniProt: P05166, propionyl-CoA carboxylase

-
Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Propionyl-CoA carboxylase / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 290980 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029034
ELECTRON MICROSCOPYf_angle_d0.52412226
ELECTRON MICROSCOPYf_dihedral_angle_d4.1391247
ELECTRON MICROSCOPYf_chiral_restr0.0451390
ELECTRON MICROSCOPYf_plane_restr0.0041587

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more