[English] 日本語
Yorodumi
- PDB-1srq: Crystal Structure of the Rap1GAP catalytic domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1srq
TitleCrystal Structure of the Rap1GAP catalytic domain
ComponentsGTPase-activating protein 1
KeywordsSIGNALING PROTEIN / MIXED ALPHA-BETA
Function / homology
Function and homology information


negative regulation of microvillus assembly / negative regulation of thyroid gland epithelial cell proliferation / cellular response to glial cell derived neurotrophic factor / Rap1 signalling / regulation of small GTPase mediated signal transduction / regulation of GTPase activity / RET signaling / negative regulation of neuron differentiation / GTPase activator activity / positive regulation of GTPase activity ...negative regulation of microvillus assembly / negative regulation of thyroid gland epithelial cell proliferation / cellular response to glial cell derived neurotrophic factor / Rap1 signalling / regulation of small GTPase mediated signal transduction / regulation of GTPase activity / RET signaling / negative regulation of neuron differentiation / GTPase activator activity / positive regulation of GTPase activity / small GTPase binding / adaptive immune response / early endosome / axon / Golgi membrane / GTPase activity / neuronal cell body / dendrite / signal transduction / protein homodimerization activity / membrane / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #210 / Arylsulfatase, C-terminal domain - #160 / Rap/Ran-GAP / Rap/Ran-GAP protein dimerization domain / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / GoLoco motif / GoLoco motif ...Helix Hairpins - #210 / Arylsulfatase, C-terminal domain - #160 / Rap/Ran-GAP / Rap/Ran-GAP protein dimerization domain / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Arylsulfatase, C-terminal domain / Helix Hairpins / Helix non-globular / Special / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Rap1 GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.9 Å
AuthorsDaumke, O. / Weyand, M. / Chakrabarti, P.P. / Vetter, I.R. / Wittinghofer, A.
CitationJournal: Nature / Year: 2004
Title: The GTPase activating protein Rap1GAP uses a catalytic asparagine
Authors: Daumke, O. / Weyand, M. / Chakrabarti, P.P. / Vetter, I.R. / Wittinghofer, A.
History
DepositionMar 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GTPase-activating protein 1
B: GTPase-activating protein 1
C: GTPase-activating protein 1
D: GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,2628
Polymers155,8334
Non-polymers4284
Water84747
1
A: GTPase-activating protein 1
B: GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1314
Polymers77,9172
Non-polymers2142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-45 kcal/mol
Surface area31150 Å2
MethodPISA
2
C: GTPase-activating protein 1
D: GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1314
Polymers77,9172
Non-polymers2142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-42 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.7, 224.5, 48.7
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

-
Components

#1: Protein
GTPase-activating protein 1 / Rap1GAP


Mass: 38958.301 Da / Num. of mol.: 4 / Fragment: Residues 75-415, catalytic fragment / Mutation: Q204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1GA1 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P47736
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: PEG 3350, MPD, magnesium sulfate, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2003 / Details: mirrors
RadiationMonochromator: Sagitally focusing Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 42290 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 71 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.06 / Net I/σ(I): 17.2
Reflection shellResolution: 2.9→2.972 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.86 / Num. unique all: 4032 / Rsym value: 0.345 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
SHARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.9→14.99 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.896 / SU B: 16.114 / SU ML: 0.308 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.743 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2103 5 %RANDOM
Rwork0.23179 ---
all0.234 40001 --
obs0.234 40001 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.265 Å2
Baniso -1Baniso -2Baniso -3
1--5.69 Å20 Å20 Å2
2--4.37 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8168 0 26 47 8241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228383
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.95211342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg451006
X-RAY DIFFRACTIONr_chiral_restr0.1360.21258
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026350
X-RAY DIFFRACTIONr_nbd_refined0.2470.23563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3860.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.25
X-RAY DIFFRACTIONr_mcbond_it0.3751.55104
X-RAY DIFFRACTIONr_mcangle_it0.68828210
X-RAY DIFFRACTIONr_scbond_it1.21233279
X-RAY DIFFRACTIONr_scangle_it1.9214.53132
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 153
Rwork0.327 2813
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)
17.08423.0740.04413.71981.00096.7805-0.28760.7310.4947-0.20060.2260.4129-0.3872-0.63090.06160.3572-0.1007-0.01720.29050.07880.3275136.3322188.302958.2725
216.16237.01611.74915.35671.05545.5711-0.00350.8673-2.04410.35950.2969-1.2290.71260.4225-0.29340.4412-0.0258-0.01340.07280.0320.4859148.5732180.2362.3395
35.55330.46950.87044.8398-0.20713.7182-0.0242-0.68020.25610.3256-0.05990.0819-0.07640.30180.08420.3557-0.23420.00560.35160.13760.1011159.3769202.726287.1113
414.08924.4812-0.76397.2341-2.19566.30010.0136-0.4119-3.6741-0.072-0.0188-0.52591.46390.10410.00520.7158-0.2391-0.03020.26280.1431.3189126.0867164.580463.169
518.95099.4855-2.74377.09851.51927.1988-1.06011.8882-1.5915-0.74030.9448-0.04710.4937-0.80680.11530.5388-0.3788-0.03260.6686-0.03910.7303116.45169.786753.719
615.09470.2313-5.20636.34662.04857.5875-0.17550.9181.24030.6692-0.4750.351-0.035-1.22760.65050.6746-0.1290.00220.50940.13411.005188.9981162.405773.1984
73.8337-0.5246-1.7595.7232-0.484310.08990.0612-0.09640.3125-0.27690.2241-0.96220.62511.4396-0.28520.26030.13080.02260.7454-0.13970.4572132.2784128.11645.4888
823.2556-2.346-6.15422.0104-1.177112.09940.1546-0.19991.60830.08480.6293-0.6708-1.08110.6563-0.78390.39-0.04250.00270.3617-0.3020.4853124.954140.031849.7576
94.61860.1945-0.17014.46570.26563.32220.1266-0.0591-0.39330.33030.0030.12580.0433-0.0311-0.12960.39050.1474-0.05730.29560.03150.1247105.5714126.639273.869
1012.0745-5.65270.69989.27760.44786.39630.0673-0.66672.46860.47460.8752-3.0279-0.89581.3563-0.94250.6129-0.14170.20121.6294-0.46262.1526150.1387137.160945.3397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA78 - 1744 - 100
2X-RAY DIFFRACTION2AA175 - 186101 - 112
3X-RAY DIFFRACTION2AA381 - 413307 - 339
4X-RAY DIFFRACTION3AA187 - 380113 - 306
5X-RAY DIFFRACTION4BB79 - 1745 - 100
6X-RAY DIFFRACTION5BB175 - 186101 - 112
7X-RAY DIFFRACTION5BB381 - 411307 - 337
8X-RAY DIFFRACTION6BB187 - 380113 - 306
9X-RAY DIFFRACTION7CC77 - 1743 - 100
10X-RAY DIFFRACTION8CC175 - 186101 - 112
11X-RAY DIFFRACTION8CC381 - 409307 - 335
12X-RAY DIFFRACTION9CC187 - 380113 - 306
13X-RAY DIFFRACTION10DD90 - 10316 - 29
14X-RAY DIFFRACTION10DD113 - 12039 - 46
15X-RAY DIFFRACTION10DD126 - 13152 - 57
16X-RAY DIFFRACTION10DD151 - 15477 - 80
17X-RAY DIFFRACTION10DD168 - 18694 - 112
18X-RAY DIFFRACTION10DD395 - 409321 - 335

+
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://pdbjlvh1.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