[English] 日本語
Yorodumi
- PDB-4c9g: Structure of yeast mitochondrial ADP/ATP carrier isoform 2 inhibi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c9g
TitleStructure of yeast mitochondrial ADP/ATP carrier isoform 2 inhibited by carboxyatractyloside (C2221 crystal form)
ComponentsADP, ATP CARRIER PROTEIN 2
KeywordsTRANSPORT PROTEIN / MITOCHONDRIAL CARRIER / ADP/ATP CARRIER
Function / homology
Function and homology information


Mitochondrial Uncoupling / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / ADP transport / mitochondrial ADP transmembrane transport / Mitochondrial protein import / ATP:ADP antiporter activity / mitochondrial ATP transmembrane transport / heme transport / ATP transport / Mitochondrial protein degradation ...Mitochondrial Uncoupling / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / ADP transport / mitochondrial ADP transmembrane transport / Mitochondrial protein import / ATP:ADP antiporter activity / mitochondrial ATP transmembrane transport / heme transport / ATP transport / Mitochondrial protein degradation / cardiolipin binding / anaerobic respiration / peroxisomal membrane / mitochondrial transport / ATPase-coupled transmembrane transporter activity / aerobic respiration / transmembrane transport / mitochondrial inner membrane / apoptotic process / mitochondrion / membrane
Similarity search - Function
ADP/ATP carrier protein, eukaryotic type / Mitochondrial carrier fold / Mitochondrial carrier domain / Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
CARDIOLIPIN / Carboxyatractyloside / ADP,ATP carrier protein 2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsRuprecht, J.J. / Hellawell, A.M. / Harding, M. / Crichton, P.G. / McCoy, A.J. / Kunji, E.R.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of Yeast Mitochondrial Adp/ATP Carriers Support a Domain-Based Alternating-Access Transport Mechanism
Authors: Ruprecht, J.J. / Hellawell, A.M. / Harding, M. / Crichton, P.G. / Mccoy, A.J. / Kunji, E.R.S.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP, ATP CARRIER PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9386
Polymers34,4681
Non-polymers5,4695
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.900, 105.670, 98.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein ADP, ATP CARRIER PROTEIN 2 / ADP/ATP TRANSLOCASE 2 / ADENINE NUCLEOTIDE TRANSLOCATOR 2 / ANT 2 / PETITE COLONIES PROTEIN 9 / ADP- ...ADP/ATP TRANSLOCASE 2 / ADENINE NUCLEOTIDE TRANSLOCATOR 2 / ANT 2 / PETITE COLONIES PROTEIN 9 / ADP-ATP CARRIER ISOFORM 2


Mass: 34468.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PYES3 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): WB12 / References: UniProt: P18239
#2: Chemical ChemComp-CXT / Carboxyatractyloside


Mass: 770.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H46O18S2
#3: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#4: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Nonpolymer detailsCARDIOLIPIN (CDL): CARDIOLIPIN ACYL CHAINS ARE MODELLED IN PART

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS PH 8.5, 10MM SODIUM CITRATE, 8% T-BUTANOL, 28% PEG600, 0.2% (W/V) NONYL GLUCOSIDE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.49→36.05 Å / Num. obs: 12639 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 5.7 % / Biso Wilson estimate: 55.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.3
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKC

1okc


Resolution: 2.49→36.047 Å / SU ML: 0.43 / σ(F): 1.37 / Phase error: 32.52 / Stereochemistry target values: ML
Details: RESIDUES 160-167 AND 215-227 ARE UNMODELLED OWING TO POOR DENSITY
RfactorNum. reflection% reflection
Rfree0.2973 1138 4.8 %
Rwork0.259 --
obs0.2608 12532 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→36.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 175 0 2160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032196
X-RAY DIFFRACTIONf_angle_d0.9072972
X-RAY DIFFRACTIONf_dihedral_angle_d17.254823
X-RAY DIFFRACTIONf_chiral_restr0.06334
X-RAY DIFFRACTIONf_plane_restr0.002359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.60330.40481600.35632768X-RAY DIFFRACTION100
2.6033-2.74050.35071460.32992771X-RAY DIFFRACTION100
2.7405-2.91210.3681360.28072838X-RAY DIFFRACTION100
2.9121-3.13690.33411500.2882803X-RAY DIFFRACTION100
3.1369-3.45230.28441440.25732808X-RAY DIFFRACTION100
3.4523-3.95130.33931300.2552829X-RAY DIFFRACTION100
3.9513-4.97620.28121170.23572818X-RAY DIFFRACTION100
4.9762-36.0510.24031550.2442792X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3888-0.3083-0.89230.40640.11774.09320.3272-0.51640.27020.7085-0.14740.2185-0.90610.2685-0.70951.2556-0.17530.87550.7218-0.09261.036413.190623.8435-5.3274
20.26360.1094-0.4142.1397-0.0421.06330.4617-0.14710.37242.0281-0.28751.4108-0.17520.0103-0.09190.9935-0.11280.25690.5266-0.00910.692519.216522.2431-13.0477
31.8836-0.6076-0.22643.81940.48022.5773-0.1984-0.1695-0.50071.5397-0.30610.00010.90840.03940.2181.7567-0.187-0.36580.5950.11310.651425.21437.9999-7.4534
42.01940.24281.23414.8445-1.03573.7887-0.04950.30570.1368-0.07070.27920.88310.1306-0.0519-0.1740.2381-0.0810.09980.48250.03170.494217.973720.7546-23.3439
50.58760.44240.47561.18960.98071.5390.1978-0.82880.32460.4494-0.06760.3892-0.35210.1017-0.21760.8085-0.03590.91420.8134-0.08381.76816.306929.6814-9.3426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 24 THROUGH 52 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 53 THROUGH 156 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 157 THROUGH 192 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 193 THROUGH 287 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 288 THROUGH 309 )

+
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