[English] 日本語
Yorodumi
- PDB-1olz: The ligand-binding face of the semaphorins revealed by the high r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1olz
TitleThe ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D
ComponentsSEMAPHORIN 4D
KeywordsDEVELOPMENTAL PROTEIN / CD100 / SEMAPHORIN / BETA-PROPELLER / PSI DOMAIN / IG-LIKE DOMAIN / EXTRACELLULAR RECEPTOR / NEUROGENESIS / GLYCOPROTEIN DEVELOPMENTAL PROTEIN / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


leukocyte aggregation / positive regulation of inhibitory synapse assembly / regulation of cell projection organization / semaphorin receptor binding / negative regulation of peptidyl-tyrosine phosphorylation / Other semaphorin interactions / negative regulation of axon extension involved in axon guidance / bone trabecula morphogenesis / semaphorin receptor complex / positive regulation of collateral sprouting ...leukocyte aggregation / positive regulation of inhibitory synapse assembly / regulation of cell projection organization / semaphorin receptor binding / negative regulation of peptidyl-tyrosine phosphorylation / Other semaphorin interactions / negative regulation of axon extension involved in axon guidance / bone trabecula morphogenesis / semaphorin receptor complex / positive regulation of collateral sprouting / chemorepellent activity / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / neural crest cell migration / positive regulation of Rho protein signal transduction / negative chemotaxis / regulation of dendrite morphogenesis / semaphorin-plexin signaling pathway / negative regulation of osteoblast differentiation / axon guidance / positive regulation of GTPase activity / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / signaling receptor activity / regulation of cell shape / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / immune response / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Semaphorin / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. ...Semaphorin / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / PSI domain / domain found in Plexins, Semaphorins and Integrins / Immunoglobulin / Immunoglobulin domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLove, C.A. / Harlos, K. / Mavaddat, N. / Davis, S.J. / Stuart, D.I. / Jones, E.Y. / Esnouf, R.M.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: The Ligand-Binding Face of the Semaphorins Revealed by the High-Resolution Crystal Structure of Sema4D
Authors: Love, C.A. / Harlos, K. / Mavaddat, N. / Davis, S.J. / Stuart, D.I. / Jones, E.Y. / Esnouf, R.M.
History
DepositionAug 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SEMAPHORIN 4D
B: SEMAPHORIN 4D


Theoretical massNumber of molelcules
Total (without water)148,6312
Polymers148,6312
Non-polymers00
Water15,151841
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.320, 76.760, 89.410
Angle α, β, γ (deg.)77.41, 73.35, 63.57
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.50294, -0.85108, -0.15071), (-0.85918, -0.51127, 0.02002), (-0.0941, 0.11942, -0.98837)
Vector: -0.119, -0.569, 0.467)

-
Components

#1: Antibody SEMAPHORIN 4D / LEUKOCYTE ACTIVATION ANTIGEN CD100 / BB18 / A8 / GR3


Mass: 74315.547 Da / Num. of mol.: 2 / Fragment: SOLUBLE EXTRACELLULAR FRAGMENT, RESIDUES 22-677
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: Q92854
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57 %
Crystal growpH: 7.5 / Details: 0.2 M AMMONIUM FLORIDE, 20% PEG 3350, pH 7.50
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.1 MTris-HCl1droppH8.0
30.1 M1dropNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 20, 2003 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 108424 / % possible obs: 97.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 1.8 / % possible all: 90.9
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 375205 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 90.9 % / Mean I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE PROTEIN WAS PRODUCED IN A EUKARYOTIC EXPRESSION SYSTEM WHICH IS THEREFORE NOT FULLY SELENO-METHIONINE LABELLED SINCE THE EXACT COMPOSITION IS UNKNOWN, WE HAVE USED A CONSERVATIVE ...Details: THE PROTEIN WAS PRODUCED IN A EUKARYOTIC EXPRESSION SYSTEM WHICH IS THEREFORE NOT FULLY SELENO-METHIONINE LABELLED SINCE THE EXACT COMPOSITION IS UNKNOWN, WE HAVE USED A CONSERVATIVE APPROACH IN REFINEMENT AND TREATED THE RESIDUES AS STANDARD METHIONINE RESIDUES ALLOWING B FACTORS TO COMPENSATE FOR OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 5440 5 %RANDOM
Rwork0.206 ---
obs0.206 107917 96.7 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9828 0 0 841 10669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.32
X-RAY DIFFRACTIONx_mcangle_it6.33
X-RAY DIFFRACTIONx_scbond_it73
X-RAY DIFFRACTIONx_scangle_it9.53.5
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.392 589 5 %
Rwork0.342 11156 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN-REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH11.WAT
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68

+
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