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- PDB-3hm6: Crystal structure of the cytoplasmic domain of human plexin B1 -

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Basic information

Entry
Database: PDB / ID: 3hm6
TitleCrystal structure of the cytoplasmic domain of human plexin B1
Components
  • Plexin-B1
  • Unknown peptide
KeywordsSIGNALING PROTEIN / structural genomics consortium / sgc / MEMBRANE / transmembrane / receptor / Cell membrane / Glycoprotein / Phosphoprotein / Secreted
Function / homology
Function and homology information


semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding ...semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / regulation of cell migration / GTPase activator activity / neuron projection morphogenesis / positive regulation of GTPase activity / G alpha (12/13) signalling events / cell migration / transmembrane signaling receptor activity / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / extracellular region / plasma membrane
Similarity search - Function
GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain ...GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 2.402 Å
AuthorsTong, Y. / He, H. / Shen, L. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Tong, Y. / He, H. / Shen, L. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and function of the intracellular region of the plexin-b1 transmembrane receptor.
Authors: Tong, Y. / Hota, P.K. / Penachioni, J.Y. / Hamaneh, M.B. / Kim, S. / Alviani, R.S. / Shen, L. / He, H. / Tempel, W. / Tamagnone, L. / Park, H.W. / Buck, M.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Plexin-B1
C: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)75,96021
Polymers75,9602
Non-polymers019
Water66737
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.346, 74.346, 214.398
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 73644.109 Da / Num. of mol.: 1 / Fragment: Cytoplasmic domain (UNP residues 1511-2135) / Mutation: S1625T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Plasmid: pFBOH-LIC (GI:134105591) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O43157
#2: Protein/peptide Unknown peptide


Mass: 2315.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Plasmid: pFBOH-LIC (GI:134105591) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACCORDING TO THE AUTHORS CHAIN C LIKELY REPRESENTS PART OF THE PROTEIN CONSTRUCT'S N-TERMINUS. ...ACCORDING TO THE AUTHORS CHAIN C LIKELY REPRESENTS PART OF THE PROTEIN CONSTRUCT'S N-TERMINUS. DENSITY WAS DISCONTINUOUS AND THE AMINO ACID SEQUENCE OF THE FRAGMENT COULD NOT BE ASSIGNED.

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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: 2.39 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% peg-2000 mme, 0.1M TRIS, 0.2M TMAO, pH 8, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 27657 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.045 / Χ2: 1.038 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.497.60.57727030.965199.9
2.49-2.598.90.40826860.9621100
2.59-2.79.50.29627230.9821100
2.7-2.85100.19127370.9921100
2.85-3.0210.30.12727350.971100
3.02-3.2610.50.08327390.9821100
3.26-3.5810.60.04827710.9831100
3.58-4.110.60.03827871.2711100
4.1-5.1610.30.03328141.4421100
5.16-309.70.01929620.777199.2

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: For phasing, native crystals were incubated over-night in an artificial mother liquor containing 0.001 M thimerosal.

Resolution: 2.402→28.083 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.224 / SU B: 19.659 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.362 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B-factors are residuals from TLS refinement. Chain C likely represents part of the protein construct's N-terminus. Density was ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B-factors are residuals from TLS refinement. Chain C likely represents part of the protein construct's N-terminus. Density was discontinuous and the amino acid sequence of the fragment could not be assigned. O, COOT, MOLPROBITY were also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1390 5.037 %RANDOM
Rwork0.227 ---
obs0.228 27598 99.779 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.297 Å2
Baniso -1Baniso -2Baniso -3
1-0.953 Å20.476 Å20 Å2
2--0.953 Å20 Å2
3----1.429 Å2
Refinement stepCycle: LAST / Resolution: 2.402→28.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 19 37 4134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224159
X-RAY DIFFRACTIONr_bond_other_d0.0010.022741
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.975661
X-RAY DIFFRACTIONr_angle_other_deg0.89936697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65523.728169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89615675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7211525
X-RAY DIFFRACTIONr_chiral_restr0.0680.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
X-RAY DIFFRACTIONr_nbd_refined0.1960.2945
X-RAY DIFFRACTIONr_nbd_other0.1770.22644
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22037
X-RAY DIFFRACTIONr_nbtor_other0.0870.22059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.23
X-RAY DIFFRACTIONr_mcbond_it1.93222713
X-RAY DIFFRACTIONr_mcbond_other0.45421056
X-RAY DIFFRACTIONr_mcangle_it2.88634239
X-RAY DIFFRACTIONr_scbond_it1.92321656
X-RAY DIFFRACTIONr_scangle_it2.69531422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.402-2.4640.4021100.2851846199298.193
2.464-2.5310.381940.271824191999.948
2.531-2.6040.306860.2651813190099.947
2.604-2.6830.314970.2617661863100
2.683-2.7710.356930.25216891782100
2.771-2.8670.287880.2411644173399.942
2.867-2.9740.354850.24616011686100
2.974-3.0940.33790.24715251604100
3.094-3.230.246730.25314901563100
3.23-3.3850.286750.23214331508100
3.385-3.5650.238740.21713331407100
3.565-3.7780.254600.22212941354100
3.778-4.0330.269630.20812041267100
4.033-4.3490.23600.19211401200100
4.349-4.7530.218530.18710451098100
4.753-5.2950.215480.2089771025100
5.295-6.0780.307500.263855905100
6.078-7.3580.276510.245741792100
7.358-10.0670.168290.194605634100
10.067-28.0830.18220.23838342794.848
Refinement TLS params.Method: refined / Origin x: -20.2896 Å / Origin y: 29.0521 Å / Origin z: -16.9473 Å
111213212223313233
T-0.0253 Å2-0.1049 Å20.0063 Å2--0.3137 Å20.0071 Å2---0.2068 Å2
L1.1305 °2-0.0362 °2-0.5348 °2-1.4759 °2-0.3424 °2--2.6048 °2
S-0.1482 Å °0.0084 Å °-0.0426 Å °-0.2278 Å °0.0892 Å °-0.1182 Å °0.4391 Å °-0.0207 Å °0.059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1563 - 2129
2X-RAY DIFFRACTION1C1007 - 1033

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