[English] 日本語
Yorodumi
- PDB-5eh4: Crystal Structure of the Glycophorin A Transmembrane Dimer in Lip... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eh4
TitleCrystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase
ComponentsGlycophorin-A
KeywordsMEMBRANE PROTEIN / Receptor / lipidic cubic phase / peptides / transmembrane
Function / homology
Function and homology information


ankyrin-1 complex / Cell surface interactions at the vascular wall / virus receptor activity / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Glycophorin, conserved site / : / Glycophorin A / Glycophorin A signature. / Glycophorin
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Glycophorin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsCall, M.J. / Call, M.E. / Trenker, R.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1030902 Australia
Australian Research Council (ARC)FT120100145 Australia
Australian Research Council (ARC)DP11010436 Australia
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase.
Authors: Trenker, R. / Call, M.E. / Call, M.J.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycophorin-A
B: Glycophorin-A
C: Glycophorin-A
D: Glycophorin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5255
Polymers13,1684
Non-polymers3571
Water0
1
A: Glycophorin-A
B: Glycophorin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9413
Polymers6,5842
Non-polymers3571
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-12 kcal/mol
Surface area5480 Å2
MethodPISA
2
C: Glycophorin-A
D: Glycophorin-A


Theoretical massNumber of molelcules
Total (without water)6,5842
Polymers6,5842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-12 kcal/mol
Surface area5160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.195, 43.195, 129.419
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

-
Components

#1: Protein/peptide
Glycophorin-A / MN sialoglycoprotein / PAS-2 / Sialoglycoprotein alpha


Mass: 3292.054 Da / Num. of mol.: 4 / Fragment: unp residues 89-117 / Mutation: M81I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: Erythrocyte / Gene: GYPA, GPA / Plasmid: pTRPLE / Production host: Escherichia coli (E. coli) / References: UniProt: P02724
#2: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.53 % / Description: Discoid
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 20% (w/v)PEG 8000, 0.1 M sodium HEPES pH 7.5 10 mM TRIS-HCl pH 8, 40 mM NaCl
PH range: 7-8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.81→35.94 Å / Num. obs: 3581 / % possible obs: 99.5 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.3602 / Net I/σ(I): 14.6
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.862 / Mean I/σ(I) obs: 3.1 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EH6

5eh6


Resolution: 2.81→35.937 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.19 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2598 367 10.44 %
Rwork0.2278 --
obs0.2323 3515 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 2.81→35.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 25 0 945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002952
X-RAY DIFFRACTIONf_angle_d0.6381281
X-RAY DIFFRACTIONf_dihedral_angle_d12.222346
X-RAY DIFFRACTIONf_chiral_restr0.02169
X-RAY DIFFRACTIONf_plane_restr0.004150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8102-3.21570.37851160.2362996X-RAY DIFFRACTION86
3.2157-4.0470.24451220.22341046X-RAY DIFFRACTION90
4.047-21.57050.22331280.22921102X-RAY DIFFRACTION90

+
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