[English] 日本語
Yorodumi
- PDB-1afo: DIMERIC TRANSMEMBRANE DOMAIN OF HUMAN GLYCOPHORIN A, NMR, 20 STRU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1afo
TitleDIMERIC TRANSMEMBRANE DOMAIN OF HUMAN GLYCOPHORIN A, NMR, 20 STRUCTURES
ComponentsGLYCOPHORIN A
KeywordsINTEGRAL MEMBRANE PROTEIN / HUMAN GLYCOPHORIN A / TRANSMEMBRANE HELIX INTERACTIONS / MEMBRANE PROTEIN FOLDING
Function / homology
Function and homology information


ankyrin-1 complex / Cell surface interactions at the vascular wall / virus receptor activity / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / Glycophorin, conserved site / : / Glycophorin A / Glycophorin A signature. / Glycophorin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING HYBRID
AuthorsMackenzie, K.R. / Prestegard, J.H. / Engelman, D.M.
Citation
Journal: Science / Year: 1997
Title: A transmembrane helix dimer: structure and implications.
Authors: MacKenzie, K.R. / Prestegard, J.H. / Engelman, D.M.
#1: Journal: Thesis, Yale University / Year: 1996
Title: Structure Determination of the Dimeric Membrane Spanning Domain of Glycophorin a in Detergent Micelles by Triple Resonance Nuclear Magnetic Resonance Spectroscopy
Authors: Mackenzie, K.R.
#2: Journal: J.Biomol.NMR / Year: 1996
Title: Leucine Side-Chain Rotamers in a Glycophorin a Transmembrane Peptide as Revealed by Three-Bond Carbon-Carbon Couplings and 13C Chemical Shifts
Authors: Mackenzie, K.R. / Prestegard, J.H. / Engelman, D.M.
History
DepositionMar 11, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOPHORIN A
B: GLYCOPHORIN A


Theoretical massNumber of molelcules
Total (without water)8,9092
Polymers8,9092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 38LEAST RESTRAINT VIOLATIONS
Representative

-
Components

#1: Protein/peptide GLYCOPHORIN A


Mass: 4454.414 Da / Num. of mol.: 2 / Fragment: TRANSMEMBRANE PEPTIDE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: MG-T7 / Cell: ERYTHROCYTE / Cellular location: PLASMA MEMBRANE / Organ: PLASMA / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): MG-T7 / References: UniProt: P02724

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121CBCA(CO)NH
131(H)CCH-TOCSY
14115N NOESY-HSQC
15113C NOESY-HSQC
161HNHA
171SPIN-ECHO DIFF CT HSQC

-
Sample preparation

Sample conditionspH: 6 / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
Varian VARIANVarianVARIAN6002

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure calculation
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING HYBRID / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 38 / Conformers submitted total number: 20

+
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