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- PDB-1olz: The ligand-binding face of the semaphorins revealed by the high r... -

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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 / semaphorin receptor binding / Other semaphorin interactions / regulation of cell projection organization / bone trabecula morphogenesis / semaphorin receptor complex / positive regulation of collateral sprouting / neuropilin binding / chemorepellent activity ...leukocyte aggregation / positive regulation of inhibitory synapse assembly / semaphorin receptor binding / Other semaphorin interactions / regulation of cell projection organization / bone trabecula morphogenesis / semaphorin receptor complex / positive regulation of collateral sprouting / neuropilin binding / chemorepellent activity / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / Sema4D mediated inhibition of cell attachment and migration / neural crest cell migration / ossification involved in bone maturation / negative chemotaxis / regulation of dendrite morphogenesis / positive regulation of Rho protein signal transduction / semaphorin-plexin signaling pathway / negative regulation of osteoblast differentiation / positive regulation of GTPase activity / axon guidance / GABA-ergic synapse / transmembrane signaling receptor activity / regulation of cell shape / signaling receptor activity / positive regulation of protein phosphorylation / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / ciliary basal body / immune response / positive regulation of cell migration / receptor ligand activity / signaling receptor binding / intracellular membrane-bounded organelle / centrosome / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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


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

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Experimental details

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Experiment

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

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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

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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

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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

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