[English] 日本語
Yorodumi
- PDB-2c2h: CRYSTAL STRUCTURE OF THE HUMAN RAC3 IN COMPLEX WITH GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c2h
TitleCRYSTAL STRUCTURE OF THE HUMAN RAC3 IN COMPLEX WITH GDP
ComponentsRAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
KeywordsSIGNALING PROTEIN / GTPASE RAC3 / SMALL GTP BINDING PROTEIN / P21 RAC / RAS- RELATED C3 BUTULINUM TOXIN SUBSTRATE 3
Function / homology
Function and homology information


cerebral cortex GABAergic interneuron development / postsynaptic actin cytoskeleton organization / regulation of neuron maturation / regulation of neutrophil migration / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / cell projection assembly / motor neuron axon guidance / PCP/CE pathway ...cerebral cortex GABAergic interneuron development / postsynaptic actin cytoskeleton organization / regulation of neuron maturation / regulation of neutrophil migration / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / cell projection assembly / motor neuron axon guidance / PCP/CE pathway / positive regulation of cell adhesion mediated by integrin / synaptic transmission, GABAergic / establishment or maintenance of cell polarity / Rac protein signal transduction / filamentous actin / neuromuscular process controlling balance / regulation of postsynapse assembly / RAC3 GTPase cycle / homeostasis of number of cells within a tissue / positive regulation of substrate adhesion-dependent cell spreading / endomembrane system / small monomeric GTPase / actin filament organization / cell periphery / cell chemotaxis / regulation of actin cytoskeleton organization / Wnt signaling pathway / calcium-dependent protein binding / lamellipodium / regulation of cell shape / G protein activity / actin cytoskeleton organization / growth cone / cytoplasmic vesicle / cytoskeleton / postsynapse / neuron projection / intracellular signal transduction / neuronal cell body / GTPase activity / endoplasmic reticulum membrane / protein kinase binding / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...Small GTPase Rho / small GTPase Rho family profile. / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDebreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. ...Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
CitationJournal: To be Published
Title: Crystal Structure of the Human Rac3 in Complex with Gdp
Authors: Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / ...Authors: Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
History
DepositionSep 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,69532
Polymers42,7202
Non-polymers4,97630
Water2,990166
1
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,08117
Polymers21,3601
Non-polymers2,72216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,61415
Polymers21,3601
Non-polymers2,25414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.320, 110.320, 81.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1187-

CA

21B-1186-

CA

31A-2097-

HOH

41A-2104-

HOH

51A-2105-

HOH

61B-2057-

HOH

71B-2059-

HOH

81B-2060-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 3 - 177 / Label seq-ID: 3 - 177

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.16319, 0.9865, 0.0136), (0.98658, -0.16325, 0.00333), (0.00551, 0.01287, -0.9999)
Vector: 54.62536, -32.00429, 89.00022)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3 / GTPASE RAC3 / P21-RAC3


Mass: 21359.770 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60763

-
Non-polymers , 5 types, 196 molecules

#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 178 TO GLY ENGINEERED RESIDUE IN CHAIN B, CYS 178 TO GLY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.6 %
Crystal growpH: 7.5
Details: 30% MPD, 0.5 M AMMONIUM SULFATE, 0.1 M HEPES PH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0038
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0038 Å / Relative weight: 1
ReflectionResolution: 1.85→27.07 Å / Num. obs: 28734 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.99
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G4U

1g4u


Resolution: 1.85→62.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.301 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1461 5.1 %RANDOM
Rwork0.194 ---
obs0.195 27267 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.85→62.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 289 166 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222917
X-RAY DIFFRACTIONr_bond_other_d0.0010.022538
X-RAY DIFFRACTIONr_angle_refined_deg1.7732.0934052
X-RAY DIFFRACTIONr_angle_other_deg0.8435859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.595344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04723.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63515403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6211513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_nbd_refined0.2230.2630
X-RAY DIFFRACTIONr_nbd_other0.1810.22607
X-RAY DIFFRACTIONr_nbtor_refined0.1960.21401
X-RAY DIFFRACTIONr_nbtor_other0.0850.21628
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6561.51754
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04622758
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68431445
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4284.51289
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
978medium positional0.110.5
1396loose positional0.315
978medium thermal0.62
1396loose thermal0.9810
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 109
Rwork0.291 1988
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)
11.5823-1.0786-0.60732.48180.57612.0716-0.00890.1193-0.0066-0.0102-0.0385-0.04070.0933-0.03360.0474-0.08490.00380.0049-0.08260.0211-0.10313.7864-19.103332.5224
22.413-0.8352-0.35172.32270.12681.79240.04440.00620.3054-0.0033-0.05790.1854-0.0635-0.07380.01360.0095-0.0219-0.035-0.00880.01920.046238.4781-15.046956.5043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 177
2X-RAY DIFFRACTION2B3 - 177

+
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