[English] 日本語
Yorodumi
- PDB-1a7b: ENGINEERING A MISFOLDED FORM OF CD2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a7b
TitleENGINEERING A MISFOLDED FORM OF CD2
ComponentsCD2
KeywordsDOMAIN SWAPPING / CD2 / OLIGOMERIZATION / PROTEIN FOLDING / PROTEIN EVOLUTION
Function / homology
Function and homology information


natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / positive regulation of interleukin-8 production / cytoplasmic side of plasma membrane / cell-cell adhesion / receptor tyrosine kinase binding / : / cell-cell junction / positive regulation of type II interferon production ...natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / positive regulation of interleukin-8 production / cytoplasmic side of plasma membrane / cell-cell adhesion / receptor tyrosine kinase binding / : / cell-cell junction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / external side of plasma membrane / signaling receptor binding / protein kinase binding / Golgi apparatus / cell surface / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMurray, A.J. / Head, J.G. / Barker, J.J. / Brady, R.L.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Engineering an intertwined form of CD2 for stability and assembly.
Authors: Murray, A.J. / Head, J.G. / Barker, J.J. / Brady, R.L.
History
DepositionMar 10, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD2
B: CD2
C: CD2
D: CD2


Theoretical massNumber of molelcules
Total (without water)43,5934
Polymers43,5934
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: CD2
B: CD2


Theoretical massNumber of molelcules
Total (without water)21,7972
Polymers21,7972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-43 kcal/mol
Surface area10480 Å2
MethodPISA
3
C: CD2
D: CD2


Theoretical massNumber of molelcules
Total (without water)21,7972
Polymers21,7972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-43 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.270, 80.030, 80.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7508, -0.4638, 0.4704), (-0.4673, -0.1304, -0.8744), (0.4669, -0.8763, -0.1188)
Vector: 4.5613, 29.9868, 27.2894)

-
Components

#1: Protein
CD2


Mass: 10898.259 Da / Num. of mol.: 4 / Fragment: DOMAIN 1 / Mutation: DEL(M46, K47)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: T-LYMPHOCYTES / Plasmid: PGEX-2T / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P08921

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 31.8 %
Crystal growpH: 7.5 / Details: 2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
22 %PEG4001reservoir
310 %glycerol1reservoir
40.1 MNaHEPES1reservoir

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 10589 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 2.89 % / Biso Wilson estimate: 48.86 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 16.1
Reflection shellResolution: 2.08→2.15 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.57 / Rsym value: 0.295 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HNG

1hng


Resolution: 3.1→15 Å / Rfactor Rfree error: 0.0035 / Data cutoff high absF: 3.1 / Data cutoff low absF: 10 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.306 7845 5 %RANDOM
Rwork0.2389 ---
obs0.2389 7705 98.1 %-
Displacement parametersBiso mean: 28.61 Å2
Refinement stepCycle: LAST / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 0 0 2956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.272
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3.1→3.24 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3375 54 14.94 %
Rwork0.2513 807 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TOPPAR:PARHCSDX.PROTOPPAR:TOPHCSDX.PRO
X-RAY DIFFRACTION2

+
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