[English] 日本語
Yorodumi
- PDB-3x1x: Ras-related protein Rap1B with GppNHp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3x1x
TitleRas-related protein Rap1B with GppNHp
ComponentsRas-related protein Rap-1b
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates RAP1 and RAC1 / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Rap1 signalling / cellular response to gonadotropin-releasing hormone / Rap protein signal transduction / regulation of cell junction assembly / MAP2K and MAPK activation / modification of postsynaptic structure ...GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates RAP1 and RAC1 / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Rap1 signalling / cellular response to gonadotropin-releasing hormone / Rap protein signal transduction / regulation of cell junction assembly / MAP2K and MAPK activation / modification of postsynaptic structure / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / calcium-ion regulated exocytosis / negative regulation of synaptic vesicle exocytosis / response to carbohydrate / establishment of endothelial barrier / Neutrophil degranulation / regulation of establishment of cell polarity / small GTPase-mediated signal transduction / : / cellular response to cAMP / lipid droplet / small monomeric GTPase / establishment of localization in cell / GDP binding / cell-cell junction / cellular response to xenobiotic stimulus / G protein activity / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / protein-containing complex binding / GTP binding / glutamatergic synapse / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rap1 / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 ...Ras-related protein Rap1 / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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
: / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsNoguchi, H. / Ikegami, T. / Park, S.Y. / Tame, J.R.H. / Unzai, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: The structure and conformational switching of Rap1B
Authors: Noguchi, H. / Ikegami, T. / Nagadoi, A. / Kamatari, Y.O. / Park, S.Y. / Tame, J.R. / Unzai, S.
History
DepositionDec 2, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_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_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_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_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 protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6524
Polymers18,9931
Non-polymers6593
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.722, 52.460, 60.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 18993.484 Da / Num. of mol.: 1 / Fragment: RAS-RELATED PROTEIN RAP1B, UNP residues 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rap1b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62636
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 32.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 12%(w/v) PEG3350, 5mM Cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. all: 421896 / Num. obs: 421896 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 38.3
Reflection shellResolution: 1→1.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 5.1 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
MOLREPphasing
PHENIX(phenix.refine: dev_1394)refinement
HKL-2000data collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→18.902 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 3623 5.06 %
Rwork0.1959 --
obs0.1966 71626 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→18.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 34 152 1504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061368
X-RAY DIFFRACTIONf_angle_d1.2651851
X-RAY DIFFRACTIONf_dihedral_angle_d14.531520
X-RAY DIFFRACTIONf_chiral_restr0.078207
X-RAY DIFFRACTIONf_plane_restr0.004237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.9997-1.01280.23221690.2154252592
1.0128-1.02670.22491460.211255994
1.0267-1.04140.22451570.2026253392
1.0414-1.05690.21891480.2015254294
1.0569-1.07340.19721270.1892259393
1.0734-1.0910.18591430.1717257994
1.091-1.10990.17761310.1637259294
1.1099-1.130.15531420.161262395
1.13-1.15180.18031440.1576259594
1.1518-1.17530.17571460.1574261495
1.1753-1.20080.21121220.1564266696
1.2008-1.22880.16131440.163261095
1.2288-1.25950.1751750.1636262696
1.2595-1.29350.22111270.1697269496
1.2935-1.33160.19031320.1713268597
1.3316-1.37450.21221380.1699268797
1.3745-1.42370.19711360.183270897
1.4237-1.48060.20651270.1809273798
1.4806-1.5480.19161350.1819272298
1.548-1.62960.19891220.1852275398
1.6296-1.73160.21891360.1937275999
1.7316-1.86520.21141420.1997278999
1.8652-2.05270.22751480.195277899
2.0527-2.34920.2151540.2015276698
2.3492-2.9580.21021560.2258263993
2.958-18.90560.3068760.2759162954

+
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