[English] 日本語
Yorodumi
- PDB-5cs0: Crystal structure of domains AC1-AC2 of yeast acetyl-CoA carboxylase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cs0
TitleCrystal structure of domains AC1-AC2 of yeast acetyl-CoA carboxylase
ComponentsAcetyl-CoA carboxylase
KeywordsLIGASE / acetyl-CoA carboxylase
Function / homology
Function and homology information


: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity ...: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / acetyl-CoA biosynthetic process / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / protein import into nucleus / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-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
Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWei, J. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD012018 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK067238 United States
CitationJournal: Nature / Year: 2015
Title: Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer.
Authors: Wei, J. / Tong, L.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase


Theoretical massNumber of molelcules
Total (without water)55,3462
Polymers55,3462
Non-polymers00
Water81145
1
A: Acetyl-CoA carboxylase


Theoretical massNumber of molelcules
Total (without water)27,6731
Polymers27,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-CoA carboxylase


Theoretical massNumber of molelcules
Total (without water)27,6731
Polymers27,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.619, 117.619, 73.856
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Acetyl-CoA carboxylase / ACC / Fatty acid synthetase 3 / mRNA transport-defective protein 7


Mass: 27673.059 Da / Num. of mol.: 2 / Fragment: unp residues 797-1033
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ACC1, ABP2, FAS3, MTR7, YNR016C, N3175 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 90 mM Bis-tris propane and 60 mM citric acid, and 20% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionRedundancy: 21.9 % / Number: 266490 / Rmerge(I) obs: 0.19 / Χ2: 1.42 / D res high: 3 Å / D res low: 50 Å / Num. obs: 12144 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.465010.0731.76820.2
5.136.4610.1771.60822
4.485.1310.1631.58522.1
4.074.4810.2141.52322.4
3.784.0710.3041.43322.4
3.563.7810.4481.34722.5
3.383.5610.6411.32222.4
3.233.3810.9611.22422.4
3.113.2311.22222.3
33.1111.1721
ReflectionResolution: 2.5→50 Å / Num. obs: 20265 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.071 / Χ2: 1.084 / Net I/av σ(I): 18.625 / Net I/σ(I): 13.8 / Num. measured all: 84727
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.593.60.4162.620011.08299.4
2.59-2.694.30.36120311.116100
2.69-2.824.30.27720031.08999.9
2.82-2.964.30.18620371.09399.7
2.96-3.154.30.13920001.127100
3.15-3.394.30.10220341.10399.9
3.39-3.734.20.07920161.02899.9
3.73-4.274.20.06520281.00499.6
4.27-5.384.10.05920511.09599.7
5.38-5040.04820641.09898.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
Cootmodel building
REFMAC5.8.0049refinement
CNSrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→34.14 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.329 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 1036 5.1 %RANDOM
Rwork0.212 ---
obs0.2151 17154 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.49 Å2 / Biso mean: 76.687 Å2 / Biso min: 39.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 2.5→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 0 45 3415
Biso mean---58.51 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193434
X-RAY DIFFRACTIONr_bond_other_d0.0010.023468
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.984640
X-RAY DIFFRACTIONr_angle_other_deg0.79737992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7265418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12224.615143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13115650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5441514
X-RAY DIFFRACTIONr_chiral_restr0.070.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02736
X-RAY DIFFRACTIONr_mcbond_it5.2447.331687
X-RAY DIFFRACTIONr_mcbond_other5.2427.3291686
X-RAY DIFFRACTIONr_mcangle_it7.54510.992100
LS refinement shellResolution: 2.498→2.633 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 156 -
Rwork0.293 2767 -
all-2923 -
obs--99.25 %

+
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://pdbjlvh1.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