[English] 日本語
Yorodumi
- PDB-1qa9: Structure of a Heterophilic Adhesion Complex Between the Human CD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qa9
TitleStructure of a Heterophilic Adhesion Complex Between the Human CD2 and CD58(LFA-3) Counter-Receptors
Components
  • HUMAN CD2 PROTEIN
  • HUMAN CD58 PROTEIN
KeywordsIMMUNE SYSTEM / CELL ADHESION / IG-LIKE DOMAIN / CD2 / CD58
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / ficolin-1-rich granule membrane / T cell activation / secretory granule membrane / positive regulation of interleukin-8 production ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / ficolin-1-rich granule membrane / T cell activation / secretory granule membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / receptor tyrosine kinase binding / cellular response to type II interferon / cell-cell adhesion / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell-cell junction / cellular response to tumor necrosis factor / signaling receptor activity / cell surface receptor signaling pathway / external side of plasma membrane / signaling receptor binding / Neutrophil degranulation / apoptotic process / Golgi apparatus / cell surface / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane
Similarity search - Function
T-cell surface antigen CD2 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface antigen CD2 / Lymphocyte function-associated antigen 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsWang, J.-H. / Smolyar, A. / Tan, K. / Liu, J.-H. / Kim, M. / Sun, Z.J. / Wagner, G. / Reinherz, E.L.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors.
Authors: Wang, J.H. / Smolyar, A. / Tan, K. / Liu, J.H. / Kim, M. / Sun, Z.Y. / Wagner, G. / Reinherz, E.L.
#1: Journal: To be Published / Year: 1999
Title: Design and NMR Studies of a Functional Glycan-Free Adhesion Domain of the Human Cell Surface Receptor CD58
Authors: Sun, Z.-Y.J. / Dotsch, V. / Kim, M. / Li, J. / Reinherz, E.L. / Wagner, G.
History
DepositionApr 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: HUMAN CD2 PROTEIN
B: HUMAN CD58 PROTEIN
C: HUMAN CD2 PROTEIN
D: HUMAN CD58 PROTEIN


Theoretical massNumber of molelcules
Total (without water)46,0424
Polymers46,0424
Non-polymers00
Water00
1
A: HUMAN CD2 PROTEIN
B: HUMAN CD58 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0212
Polymers23,0212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HUMAN CD2 PROTEIN
D: HUMAN CD58 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0212
Polymers23,0212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.820, 33.470, 108.430
Angle α, β, γ (deg.)90.00, 121.76, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly is each of the individual molecules

-
Components

#1: Protein HUMAN CD2 PROTEIN


Mass: 12017.655 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ADHESION DOMAIN OF CD2 / Mutation: K61E, F63L, T67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: P06729*PLUS
#2: Protein HUMAN CD58 PROTEIN


Mass: 11003.180 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ADHESION DOMAIN OF CD58 / Mutation: F1S, V9K, V21Q, V58K, T85S, L93G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: P19256*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, (NH4)2SO4, NaCl, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
20.1 MHEPES1drop
32 %PEG4001reservoir
42 Mammonium sulfate1reservoir
51 M1reservoirNaCl
60.1 MHEPES1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→18 Å / Num. all: 9453 / Num. obs: 8196 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.8
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.278 / Num. unique all: 8196 / % possible all: 87.6
Reflection
*PLUS
Num. measured all: 41649
Reflection shell
*PLUS
% possible obs: 87.6 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.2→18 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflection
Rfree0.281 778 -
Rwork0.223 --
all-7780 -
obs-7486 96.2 %
Refinement stepCycle: LAST / Resolution: 3.2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 0 0 3244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.102
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / σ(F): 2 / Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.006

+
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