[English] 日本語
Yorodumi
- PDB-2rex: Crystal structure of the effector domain of PLXNB1 bound with Rnd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rex
TitleCrystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase
Components
  • Plexin-B1
  • Rho-related GTP-binding protein Rho6
KeywordsSIGNALING PROTEIN/LIPOPROTEIN / complex / Structural Genomics Consortium / SGC / gtpase / gnp / Plexin / effector domain / Glycoprotein / Membrane / Phosphorylation / Receptor / Secreted / Transmembrane / Cytoskeleton / GTP-binding / Lipoprotein / Methylation / Nucleotide-binding / Prenylation / SIGNALING PROTEIN-LIPOPROTEIN COMPLEX
Function / homology
Function and homology information


semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / inhibitory synapse assembly / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / 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 / negative regulation of osteoblast proliferation / semaphorin receptor complex / inhibitory synapse assembly / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / 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 / RND1 GTPase cycle / ossification involved in bone maturation / positive regulation of axonogenesis / small GTPase-mediated signal transduction / positive regulation of Rho protein signal transduction / neuron remodeling / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / regulation of cell migration / GTPase activator activity / neuron projection morphogenesis / positive regulation of GTPase activity / actin filament organization / regulation of actin cytoskeleton organization / adherens junction / transmembrane signaling receptor activity / G alpha (12/13) signalling events / cell migration / actin cytoskeleton / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / intracellular membrane-bounded organelle / signaling receptor binding / GTPase activity / GTP binding / protein kinase binding / signal transduction / extracellular region / plasma membrane / cytosol
Similarity search - Function
Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat ...Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / Small GTPase Rho / small GTPase Rho family profile. / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Plexin-B1 / Rho-related GTP-binding protein Rho6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsTong, Y. / Tempel, W. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase.
Authors: Tong, Y. / Tempel, W. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionSep 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,66040
Polymers70,4874
Non-polymers1,17336
Water1,35175
1
A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,83020
Polymers35,2432
Non-polymers58718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
MethodPISA
2
C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,83020
Polymers35,2432
Non-polymers58718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
MethodPISA
3
A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
hetero molecules

C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,66040
Polymers70,4874
Non-polymers1,17336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4850 Å2
MethodPISA
4
A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
hetero molecules

A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
hetero molecules

C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules

C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,32080
Polymers140,9738
Non-polymers2,34672
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_545-x,y-1,-z1
Buried area11120 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.136, 71.653, 101.885
Angle α, β, γ (deg.)90.000, 128.360, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe authors state that the relationships between chains A and B and between chains C and D of the asymmetric unit reflect the biologically relevant interface between the plexin effector domain and RND1 gtpase.

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 13297.139 Da / Num. of mol.: 2 / Fragment: Residues 1743-1862
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O43157
#2: Protein Rho-related GTP-binding protein Rho6 / Rho family GTPase 1 / Rnd1


Mass: 21946.164 Da / Num. of mol.: 2 / Fragment: Residues 5-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RND1, RHO6 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q92730

-
Non-polymers , 5 types, 111 molecules

#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 30 / Source method: obtained synthetically
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 36932 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.503 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.383.20.23132320.661184.8
2.38-2.483.40.20534860.664193.1
2.48-2.593.60.1836870.711198.1
2.59-2.733.70.15737380.786199.8
2.73-2.93.80.10637940.7381100
2.9-3.123.80.08338090.8111100
3.12-3.433.80.05937770.951199.9
3.43-3.933.80.04837861.209199.8
3.93-4.953.80.03938091.307199.9
4.95-303.60.05338146.995197.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2CLS,2R2O

2cls

2r2o


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.214 / SU B: 11.089 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B factors are residuals of TLS refinement. Programs coot, molprobity have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 999 2.71 %Thin shells
Rwork0.215 ---
all0.216 36863 --
obs0.216 36863 97.472 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.565 Å2
Baniso -1Baniso -2Baniso -3
1-5.87 Å20 Å22.92 Å2
2---2.831 Å20 Å2
3---0.585 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 0 98 75 4452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224457
X-RAY DIFFRACTIONr_bond_other_d0.0020.022906
X-RAY DIFFRACTIONr_angle_refined_deg1.4482.0046081
X-RAY DIFFRACTIONr_angle_other_deg0.9493.0017146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30324.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75215721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0821523
X-RAY DIFFRACTIONr_chiral_restr0.0810.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
X-RAY DIFFRACTIONr_nbd_refined0.1910.2781
X-RAY DIFFRACTIONr_nbd_other0.190.22988
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22071
X-RAY DIFFRACTIONr_nbtor_other0.0870.22304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2156
X-RAY DIFFRACTIONr_metal_ion_refined0.1960.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.40.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.27
X-RAY DIFFRACTIONr_mcbond_it0.5951.52917
X-RAY DIFFRACTIONr_mcbond_other0.1281.51133
X-RAY DIFFRACTIONr_mcangle_it0.93624579
X-RAY DIFFRACTIONr_scbond_it1.50831801
X-RAY DIFFRACTIONr_scangle_it2.3274.51498
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 (%)
2.3-2.35900.2312305273884.186
2.359-2.42300.2312437268690.73
2.423-2.49200.2292480260395.275
2.492-2.5670.3172270.2212251252698.1
2.567-2.6500.2152448245499.756
2.65-2.7410.2621740.2212214239299.833
2.741-2.8430.252120.21322982310100
2.843-2.95600.21222252225100
2.956-3.0850.2311670.22519572124100
3.085-3.23100.2012022202399.951
3.231-3.4010.2411270.20218291956100
3.401-3.60100.21838184399.729
3.601-3.84100.2191745175099.714
3.841-4.1360.227900.2021517160899.938
4.136-4.5110.232780.1871425150599.867
4.511-5.01200.1921375137799.855
5.012-5.7280.209540.2171165122099.918
5.728-6.8760.246350.2561032106999.813
6.876-9.1950.256200.23481884399.407
9.195-200.368150.31448356787.831
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54830.56920.47484.45852.37884.6060.0260.31610.3174-0.4669-0.0062-0.0951-0.73670.0936-0.01980.0654-0.01480.0576-0.10030.0870.048619.6909-47.23496.9249
22.74361.0575-1.53525.0421-0.16063.10130.2623-0.10670.36460.3037-0.20330.513-0.3237-0.3247-0.059-0.1152-0.00010.0226-0.0854-0.0604-0.123.7864-62.834227.5641
34.6173-1.9355-0.42893.50440.2761.4222-0.0392-0.2648-0.67220.0956-0.03790.25210.3328-0.23630.0771-0.0753-0.0715-0.0654-0.09940.0476-0.09998.6767-21.862821.0376
42.32740.333-0.91363.8074-0.99333.39890.06770.3245-0.1831-0.5172-0.1417-0.25460.20750.02620.074-0.14340.0460.0033-0.091-0.0189-0.134524.4757-6.62410.0131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1746 - 1852
2X-RAY DIFFRACTION2B13 - 188
3X-RAY DIFFRACTION3C1746 - 1852
4X-RAY DIFFRACTION4D7 - 188

+
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