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- PDB-3ol2: Receptor-ligand structure of Human Semaphorin 4D with Plexin B1. -

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Basic information

Entry
Database: PDB / ID: 3ol2
TitleReceptor-ligand structure of Human Semaphorin 4D with Plexin B1.
Components
  • Plexin-B1
  • Semaphorin-4D
KeywordsSIGNALING PROTEIN / Beta-Propeller / Signalling / Extacellular
Function / homology
Function and homology information


positive regulation of inhibitory synapse assembly / leukocyte aggregation / regulation of cell projection organization / semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis / semaphorin receptor binding / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of axon extension involved in axon guidance / Other semaphorin interactions / negative regulation of alkaline phosphatase activity / negative regulation of osteoblast proliferation ...positive regulation of inhibitory synapse assembly / leukocyte aggregation / regulation of cell projection organization / semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis / semaphorin receptor binding / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of axon extension involved in axon guidance / Other semaphorin interactions / negative regulation of alkaline phosphatase activity / negative regulation of osteoblast proliferation / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / inhibitory synapse assembly / positive regulation of collateral sprouting / Sema4D induced cell migration and growth-cone collapse / RHOD GTPase cycle / semaphorin receptor activity / ossification involved in bone maturation / chemorepellent activity / negative regulation of cell adhesion / Sema4D mediated inhibition of cell attachment and migration / neural crest cell migration / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / negative chemotaxis / GTPase activating protein binding / regulation of cytoskeleton organization / regulation of dendrite morphogenesis / negative regulation of osteoblast differentiation / regulation of GTPase activity / neuron projection morphogenesis / regulation of cell migration / GTPase activator activity / G alpha (12/13) signalling events / axon guidance / positive regulation of GTPase activity / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphatidylinositol 3-kinase signaling / cell migration / signaling receptor activity / regulation of cell shape / intracellular 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 / integral component of plasma membrane / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Semaphorin / TIG domain found in plexin / Plexin, TIG domain 2 / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin family ...Semaphorin / TIG domain found in plexin / Plexin, TIG domain 2 / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain superfamily / Sema domain / Sema domain profile. / IPT/TIG domain / Rho GTPase activation protein / ig-like, plexins, transcription factors / domain found in Plexins, Semaphorins and Integrins / PSI domain / IPT domain / Immunoglobulin / Immunoglobulin domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / WD40/YVTN repeat-like-containing domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Plexin-B1 / Semaphorin-4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsJanssen, B.J.C. / Robinson, R.A. / Perez-Branguli, F. / Bell, C.H. / Mitchell, C.J. / Siebold, C. / Jones, E.Y.
CitationJournal: Nature / Year: 2010
Title: Structural basis of semaphorin-plexin signalling.
Authors: Janssen, B.J. / Robinson, R.A. / Perez-Branguli, F. / Bell, C.H. / Mitchell, K.J. / Siebold, C. / Jones, E.Y.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Semaphorin-4D
B: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4949
Polymers131,2402
Non-polymers3,2547
Water0
1
A: Semaphorin-4D
B: Plexin-B1
hetero molecules

A: Semaphorin-4D
B: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,98918
Polymers262,4804
Non-polymers6,50814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9780 Å2
ΔGint42 kcal/mol
Surface area55420 Å2
Unit cell
Length a, b, c (Å)83.055, 173.436, 482.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
DetailsIn the native form Human semaphorin 4D exists as a dimer. / Domains 1 and 2 of Human plexin B1 are monomeric in solution.

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Components

#1: Protein Semaphorin-4D / BB18 / A8 / GR3


Mass: 74315.547 Da / Num. of mol.: 1 / Fragment: Extracellular domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEMA4D, C9orf164, CD100, SEMAJ / Production host: Homo sapiens (human) / References: UniProt: Q92854
#2: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 56924.668 Da / Num. of mol.: 1 / Fragment: Extracellular domainsl (1-2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Production host: Homo sapiens (human) / References: UniProt: O43157
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 0.1 M Tris,0.2 M calcium acetate, 6% v/v glycerol, 20% PEG3000, pH 7, VAPOR DIFFUSION, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03
DetectorDate: Oct 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.99 Å / Num. obs: 35192 / Biso Wilson estimate: 84.64 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.9.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→49.49 Å / Cor.coef. Fo:Fc: 0.9258 / Cor.coef. Fo:Fc free: 0.8966 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1760 5 %RANDOM
Rwork0.1895 ---
obs0.192 35192 --
Displacement parametersBiso mean: 75.89 Å2
Baniso -1Baniso -2Baniso -3
1--15.9027 Å20 Å20 Å2
2--0.6743 Å20 Å2
3---15.2283 Å2
Refine analyzeLuzzati coordinate error obs: 0.415 Å
Refinement stepCycle: LAST / Resolution: 2.99→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8613 0 215 0 8828
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019074HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2812378HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2946SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes215HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1477HARMONIC5
X-RAY DIFFRACTIONt_it9074HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion19.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1197SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9896SEMIHARMONIC4
LS refinement shellResolution: 2.99→3.08 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3926 114 4.34 %
Rwork0.2487 2515 -
all0.2548 2629 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4809-0.1186-0.5650.84460.32.1952-0.2444-0.0911-0.27630.18960.09620.17040.4173-0.41570.1482-0.0519-0.06880.1219-0.16330.0293-0.1418-5.244-23.69665.3999
23.68990.7924-2.8180.0054-0.26951.0612-0.0273-0.1243-0.0323-0.0399-0.0450.20450.0866-0.09170.0723-0.0054-0.10120.1520.3040.0847-0.304-26.7491-18.387993.2957
31.10670.0182-2.60661.91171.49135.8620.0343-0.30730.0486-0.069-0.0626-0.0134-0.11290.26510.0282-0.16060.0560.14870.3040.0006-0.304-13.6636-1.3135110.844
40.9115-0.2421-0.58750.67690.15392.12220.0582-0.06240.2267-0.0310.1278-0.05630.0047-0.0844-0.186-0.0291-0.06690.0616-0.204-0.0313-0.010522.7015-20.826429.0035
53.70050.1975-0.22920.12632.89675.60790.07920.0960.06740.0993-0.0502-0.24560.02050.26-0.0290.0895-0.06550.152-0.0086-0.1304-0.024154.6079-19.17929.3861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|24 - A|501 A|1000 - A|9001 }A24 - 501
2X-RAY DIFFRACTION1{ A|24 - A|501 A|1000 - A|9001 }A1000 - 9001
3X-RAY DIFFRACTION2{ A|502 - A|552 }A502 - 552
4X-RAY DIFFRACTION3{ A|553 - A|648 }A553 - 648
5X-RAY DIFFRACTION4{ B|23 - B|487 B|2000 - B|2002 }B23 - 487
6X-RAY DIFFRACTION4{ B|23 - B|487 B|2000 - B|2002 }B2000 - 2002
7X-RAY DIFFRACTION5{ B|488 - B|533 }B488 - 533

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