[English] 日本語
Yorodumi
- PDB-3sua: Crystal structure of the intracellular domain of Plexin-B1 in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sua
TitleCrystal structure of the intracellular domain of Plexin-B1 in complex with Rac1
Components
  • Plexin-B1
  • Ras-related C3 botulinum toxin substrate 1
KeywordsAPOPTOSIS/SIGNALING PROTEIN / Axon guidance / signal transduction / APOPTOSIS-SIGNALING PROTEIN complex
Function / homology
Function and homology information


semaphorin receptor binding / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration ...semaphorin receptor binding / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / negative regulation of osteoblast proliferation / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / interneuron migration / kinocilium / regulation of cell adhesion involved in heart morphogenesis / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / cochlea morphogenesis / regulation of neuron maturation / semaphorin receptor complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of skeletal muscle acetylcholine-gated channel clustering / hepatocyte growth factor receptor signaling pathway / GTP-dependent protein binding / semaphorin receptor activity / midbrain dopaminergic neuron differentiation / ruffle organization / epithelial cell morphogenesis / cell projection assembly / positive regulation of bicellular tight junction assembly / negative regulation of cell adhesion / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / regulation of neuron migration / negative regulation of fibroblast migration / RHO GTPases activate CIT / GTPase activating protein binding / RHOD GTPase cycle / cell-cell junction organization / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / motor neuron axon guidance / positive regulation of axonogenesis / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / Activation of RAC1 / inhibitory synapse assembly / MET activates RAP1 and RAC1 / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / positive regulation of cell-substrate adhesion / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / ossification involved in bone maturation / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / NRAGE signals death through JNK / dendrite morphogenesis / regulation of cell size / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / positive regulation of dendritic spine development / synaptic transmission, GABAergic / regulation of cytoskeleton organization / positive regulation of actin filament polymerization / Rac protein signal transduction / pericentriolar material / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / neuron projection morphogenesis / ficolin-1-rich granule membrane / regulation of postsynapse assembly / Sema3A PAK dependent Axon repulsion / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / positive regulation of GTPase activity
Similarity search - Function
Plexin-B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / 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-B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / 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 domain profile. / ig-like, plexins, transcription factors / Rho GTPase activation protein / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Plexin-B1 / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.39 Å
AuthorsBell, C.H. / Aricescu, A.R. / Jones, E.Y. / Siebold, C.
CitationJournal: Plos Biol. / Year: 2011
Title: A Dual Binding Mode for RhoGTPases in Plexin Signalling.
Authors: Bell, C.H. / Aricescu, A.R. / Jones, E.Y. / Siebold, C.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1
B: Ras-related C3 botulinum toxin substrate 1
C: Ras-related C3 botulinum toxin substrate 1
D: Plexin-B1
E: Plexin-B1
F: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,53012
Polymers279,8916
Non-polymers1,6406
Water00
1
A: Ras-related C3 botulinum toxin substrate 1
D: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8434
Polymers93,2972
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-25 kcal/mol
Surface area32190 Å2
MethodPISA
2
B: Ras-related C3 botulinum toxin substrate 1
E: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8434
Polymers93,2972
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-25 kcal/mol
Surface area32330 Å2
MethodPISA
3
C: Ras-related C3 botulinum toxin substrate 1
F: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8434
Polymers93,2972
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-25 kcal/mol
Surface area32380 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-97 kcal/mol
Surface area91780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.340, 224.250, 258.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

-
Components

#1: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 20668.826 Da / Num. of mol.: 3 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000
#2: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 72628.016 Da / Num. of mol.: 3 / Fragment: UNP residues 1533-2135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43157
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
Sequence detailsS1625T CONFLICT IN UNP ENTRY O43157

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.58 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 4.39→50 Å / Num. obs: 25525 / Biso Wilson estimate: 171.72 Å2

-
Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.39→47.81 Å / Cor.coef. Fo:Fc: 0.7814 / Cor.coef. Fo:Fc free: 0.7482 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 1318 5.16 %RANDOM
Rwork0.2336 ---
obs0.2351 25522 --
all-25522 --
Displacement parametersBiso mean: 124.57 Å2
Baniso -1Baniso -2Baniso -3
1-37.5289 Å20 Å20 Å2
2--16.0763 Å20 Å2
3----53.6052 Å2
Refine analyzeLuzzati coordinate error obs: 1.106 Å
Refinement stepCycle: LAST / Resolution: 4.39→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16394 0 99 0 16493
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00916840HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1622892HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5886SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes396HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2378HARMONIC5
X-RAY DIFFRACTIONt_it16840HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion22.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2194SEMIHARMONIC5
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_contact19665SEMIHARMONIC4
LS refinement shellResolution: 4.39→4.57 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2673 137 4.89 %
Rwork0.2513 2662 -
all0.2521 2799 -
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)
10.659-0.00471.16530.32291.128100.09550.182-0.12180.2568-0.04830.01480.0246-0.0151-0.0473-0.0341-0.1484-0.2226-0.06550.19260.0478-2.144233.848-17.7339
23.12660.7293-1.5881.0941-0.22850.3920.60410.17320.7204-0.2524-0.1196-0.32130.0926-0.3406-0.4844-0.4470.11540.304-0.1550.04310.6079-20.593686.0822-60.6926
30-1.6995-0.80351.41150.60950.06780.2434-0.2716-0.0255-0.3332-0.2413-0.1988-0.1028-0.2214-0.0021-0.26110.13970.0796-0.1786-0.08410.4569-20.087417.6546-84.8482
401.4701-2.27681.7865-2.879800.21780.2359-0.00310.5554-0.14960.2615-0.30320.1834-0.0682-0.09860.1831-0.07710.1801-0.2077-0.148-32.266356.9827-24.6399
50-0.5380.75553.00350.676300.22370.16050.15570.37210.1939-0.04660.20440.1632-0.4176-0.41890.07560.0042-0.1121-0.12460.5297-44.448257.261-71.6564
62.81680.06090.5910.08320.35372.11620.35920.13670.13460.2041-0.4665-0.22560.133-0.19440.1073-0.2654-0.1101-0.0295-0.2076-0.01620.3462-33.913914.9102-48.8671
70-0.3191-0.22170-0.13731.4689-0.15950.06680.04730.38190.3409-0.43550.2273-0.5275-0.1813-0.31510.3040.28090.4337-0.1413-0.0493-52.994680.274-26.57
82.44430.0421-1.51962.95670.55930.56320.23530.5564-0.11150.55260.16550.0406-0.2129-0.0358-0.4008-0.52690.1616-0.05070.0546-0.12890.2142-62.944436.3024-85.4289
900.6148-1.47550-0.29150.0688-0.19730.3674-0.14080.28790.3539-0.07620.1071-0.2288-0.1566-0.1479-0.3040.3040.2050.21260.0901-43.56727.6169-20.1306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ D|1563 - D|1745 D|1916 - D|2023 D|2033 - D|2129 }D1563 - 1745
2X-RAY DIFFRACTION1{ D|1563 - D|1745 D|1916 - D|2023 D|2033 - D|2129 }D1916 - 2023
3X-RAY DIFFRACTION1{ D|1563 - D|1745 D|1916 - D|2023 D|2033 - D|2129 }D2033 - 2129
4X-RAY DIFFRACTION2{ E|1563 - E|1745 E|1914 - E|2023 E|2033 - E|2129 }E1563 - 1745
5X-RAY DIFFRACTION2{ E|1563 - E|1745 E|1914 - E|2023 E|2033 - E|2129 }E1914 - 2023
6X-RAY DIFFRACTION2{ E|1563 - E|1745 E|1914 - E|2023 E|2033 - E|2129 }E2033 - 2129
7X-RAY DIFFRACTION3{ F|1563 - F|1745 F|1913 - F|2023 F|2033 - F|2129 }F1563 - 1745
8X-RAY DIFFRACTION3{ F|1563 - F|1745 F|1913 - F|2023 F|2033 - F|2129 }F1913 - 2023
9X-RAY DIFFRACTION3{ F|1563 - F|1745 F|1913 - F|2023 F|2033 - F|2129 }F2033 - 2129
10X-RAY DIFFRACTION4{ D|1746 - D|1757 D|1764 - D|1854 D|1880 - D|1890 }D1746 - 1757
11X-RAY DIFFRACTION4{ D|1746 - D|1757 D|1764 - D|1854 D|1880 - D|1890 }D1764 - 1854
12X-RAY DIFFRACTION4{ D|1746 - D|1757 D|1764 - D|1854 D|1880 - D|1890 }D1880 - 1890
13X-RAY DIFFRACTION5{ E|1746 - E|1757 E|1764 - E|1854 E|1880 - E|1890 }E1746 - 1757
14X-RAY DIFFRACTION5{ E|1746 - E|1757 E|1764 - E|1854 E|1880 - E|1890 }E1764 - 1854
15X-RAY DIFFRACTION5{ E|1746 - E|1757 E|1764 - E|1854 E|1880 - E|1890 }E1880 - 1890
16X-RAY DIFFRACTION6{ F|1746 - F|1757 F|1764 - F|1854 F|1880 - F|1890 }F1746 - 1757
17X-RAY DIFFRACTION6{ F|1746 - F|1757 F|1764 - F|1854 F|1880 - F|1890 }F1764 - 1854
18X-RAY DIFFRACTION6{ F|1746 - F|1757 F|1764 - F|1854 F|1880 - F|1890 }F1880 - 1890
19X-RAY DIFFRACTION7{ A|1 - A|178 A|200 - A|201 }A1 - 178
20X-RAY DIFFRACTION7{ A|1 - A|178 A|200 - A|201 }A200 - 201
21X-RAY DIFFRACTION8{ B|1 - B|178 B|200 - B|201 }B1 - 178
22X-RAY DIFFRACTION8{ B|1 - B|178 B|200 - B|201 }B200 - 201
23X-RAY DIFFRACTION9{ C|1 - C|178 C|200 - C|201 }C1 - 178
24X-RAY DIFFRACTION9{ C|1 - C|178 C|200 - C|201 }C200 - 201

+
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