[English] 日本語
Yorodumi
- PDB-7vvb: Crystal Structure of KRas4A(GMPPNP-bound) in complex with the Ras... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vvb
TitleCrystal Structure of KRas4A(GMPPNP-bound) in complex with the Ras-binding domain(RBD) of SIN1
Components
  • GTPase KRas
  • Target of rapamycin complex 2 subunit MAPKAP1
KeywordsCELL CYCLE / Ras / RBD
Function / homology
Function and homology information


TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / negative regulation of Ras protein signal transduction / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation ...TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / negative regulation of Ras protein signal transduction / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Constitutive Signaling by AKT1 E17K in Cancer / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / cellular response to nutrient levels / CD28 dependent PI3K/Akt signaling / phosphatidylinositol-3,4,5-trisphosphate binding / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / cytoskeleton organization / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / phosphatidylinositol-4,5-bisphosphate binding / EGFR Transactivation by Gastrin / substantia nigra development / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / G protein activity / VEGFR2 mediated vascular permeability / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / small GTPase binding / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants
Similarity search - Function
Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / 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 / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas / Target of rapamycin complex 2 subunit MAPKAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZheng, Y.Y. / Zhou, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural insights into Ras regulation by SIN1.
Authors: Zheng, Y. / Ding, L. / Meng, X. / Potter, M. / Kearney, A.L. / Zhang, J. / Sun, J. / James, D.E. / Yang, G. / Zhou, C.
History
DepositionNov 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Target of rapamycin complex 2 subunit MAPKAP1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4974
Polymers80,9512
Non-polymers5472
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.660, 101.660, 124.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

-
Components

#1: Protein Target of rapamycin complex 2 subunit MAPKAP1 / TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated ...TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated map kinase-interacting protein 1 / SAPK-interacting protein 1 / mSIN1


Mass: 59206.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP1, MIP1, SIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BPZ7
#2: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21743.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, small monomeric GTPase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.15 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→22.38 Å / Num. obs: 79142 / % possible obs: 99.78 % / Redundancy: 18.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0682 / Net I/σ(I): 26.68
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 15.8 % / Rmerge(I) obs: 0.5955 / Num. unique obs: 4143 / CC1/2: 0.949 / % possible all: 99.98

-
Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G0N

4g0n


Resolution: 1.7→22.38 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 3811 4.82 %
Rwork0.1727 75331 -
obs0.1739 79142 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.99 Å2 / Biso mean: 33.0566 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 1.7→22.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 33 257 2244
Biso mean--22.48 43.02 -
Num. residues----244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.720.29361340.25622823100
1.72-1.740.25941540.24772797100
1.74-1.770.24241610.21592743100
1.77-1.790.24281350.21822812100
1.79-1.820.191180.20782819100
1.82-1.850.24291330.19522821100
1.85-1.880.23761480.19982764100
1.88-1.910.2681510.19542774100
1.91-1.950.24871670.19582742100
1.95-1.980.21161710.19392783100
1.98-2.020.24881310.19682786100
2.02-2.070.21041370.18562809100
2.07-2.120.20891280.17882812100
2.12-2.170.20271650.18282764100
2.17-2.230.19111410.17862796100
2.23-2.290.22191310.16822802100
2.29-2.370.22031470.16892771100
2.37-2.450.19861510.17892778100
2.45-2.550.20921600.18082781100
2.55-2.670.17531300.182818100
2.67-2.810.2361400.18562784100
2.81-2.980.16751060.18562828100
2.98-3.210.19591470.15882780100
3.21-3.530.16071310.15972792100
3.53-4.040.17831320.1463278599
4.05-5.090.16531330.14272801100
5.09-22.380.20071290.1838276699
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)
14.444-3.60130.77072.99680.09892.8379-0.01170.55910.7454-0.1783-0.0862-0.5062-0.38530.03230.10710.1779-0.01790.01070.20870.07420.2632-26.464354.2417-1.4094
25.5509-4.95070.08749.13920.76644.00590.44360.92810.1944-0.8293-0.595-0.2722-0.20260.05880.15610.32730.00410.01710.48250.06740.2424-30.729451.4824-8.5206
35.35942.68711.47363.00072.14092.5019-0.4436-0.2378-0.3413-0.4130.20930.3056-0.4123-0.38160.56940.73790.2189-0.19111.047-0.18640.4278-36.907245.5277-13.822
45.6686-1.0096-1.17074.10281.8532.25220.33590.1984-0.25250.5077-0.12010.31040.055-0.4845-0.10520.17230.0371-0.02110.39990.00220.2621-38.9951.4801-1.4741
54.37510.57080.79632.8985-0.85694.129-0.04740.13710.3323-0.11440.15550.4333-0.3256-0.5158-0.05940.24690.0507-0.01820.32440.0110.2844-39.828257.2580.8079
66.9901-4.06441.33195.91750.17455.7581-0.713-0.3981.17620.77160.2911-0.3555-1.4999-0.09920.42940.37870.0226-0.08940.2272-0.00110.2988-31.683462.4922.8793
78.6125-1.73370.88553.5915-3.01267.29250.048-0.013-0.83250.2520.02680.11090.335-0.49810.08950.17720.01530.00870.3051-0.02210.266-36.063949.114-0.0239
86.41090.42944.7731.6117-0.42686.51720.19920.62570.2867-0.6855-0.02590.96070.3364-0.6805-0.22970.5067-0.0495-0.01110.5708-0.0380.5634-43.121345.3258-0.886
91.76040.0275-0.16932.7913-0.65822.7834-0.07770.4459-0.18250.10770.15360.08790.0744-0.4887-0.07570.1328-0.03640.01640.2637-0.02340.1854-19.765235.7318-3.4812
103.29660.58070.50945.46423.3594.9371-0.00761.08260.4538-0.4307-0.35850.6415-0.32-0.49960.19660.21630.00750.02270.54940.07560.3625-19.448744.3557-12.9474
112.2052.1179-0.19547.1687-0.51.852-0.00980.0497-0.03360.0087-0.001-0.02860.1096-0.0656-0.0130.1887-0.03790.01440.26590.00180.1941-23.452834.1131-0.908
123.7470.33730.92218.5805-3.83135.8276-0.2220.23980.77840.35230.1326-0.2492-0.7946-0.17090.23470.3921-0.0488-0.0350.4113-0.05240.3822-12.580346.43375.9475
133.3471.3889-4.00051.4412-1.20926.28550.0281-0.02070.04480.07770.0096-0.11820.01760.0208-0.0470.1511-0.012-0.00110.29160.00910.2341-8.866536.2184-4.4289
142.81030.1314-3.41440.6665-0.77534.34880.2261-0.7694-0.03960.3685-0.1937-0.4315-0.64691.61050.00580.2322-0.0758-0.05460.4124-0.02910.3222-2.476339.92171.8506
152.0156-0.5627-1.21611.88810.8526.9905-0.094-0.1843-0.22390.21940.0847-0.2820.54720.8640.1090.1940.0011-0.02110.29320.01050.2906-7.91931.89174.4656
163.45010.38731.14060.11480.46651.7708-0.00761.4701-0.3782-0.3462-0.1342-0.22490.4263-0.17350.19110.2558-0.03770.08130.5738-0.06070.3584-3.766335.0654-17.6657
174.55220.6538-2.35733.090.43892.085-0.2831-0.4141-0.76170.05290.314-0.14910.73120.64910.02570.23280.04620.0120.35630.02440.351.993628.6208-4.5574
186.7916-2.38993.03273.8646-2.40486.64960.19210.9897-0.8966-0.3691-0.09620.30590.60670.1858-0.02820.2209-0.06330.05290.38-0.0730.3004-11.300429.3534-11.2138
194.09931.46920.01933.756-0.57978.1252-0.307-0.0264-0.7408-0.11220.048-0.79681.11890.30920.24580.2787-0.04750.06750.2707-0.02030.4009-16.621125.0762-0.1618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 278 through 300 )B278 - 300
2X-RAY DIFFRACTION2chain 'B' and (resid 301 through 313 )B301 - 313
3X-RAY DIFFRACTION3chain 'B' and (resid 314 through 322 )B314 - 322
4X-RAY DIFFRACTION4chain 'B' and (resid 323 through 327 )B323 - 327
5X-RAY DIFFRACTION5chain 'B' and (resid 328 through 340 )B328 - 340
6X-RAY DIFFRACTION6chain 'B' and (resid 341 through 347 )B341 - 347
7X-RAY DIFFRACTION7chain 'B' and (resid 348 through 353 )B348 - 353
8X-RAY DIFFRACTION8chain 'B' and (resid 354 through 358 )B354 - 358
9X-RAY DIFFRACTION9chain 'A' and (resid 0 through 25 )A0 - 25
10X-RAY DIFFRACTION10chain 'A' and (resid 26 through 36 )A26 - 36
11X-RAY DIFFRACTION11chain 'A' and (resid 37 through 61 )A37 - 61
12X-RAY DIFFRACTION12chain 'A' and (resid 62 through 74 )A62 - 74
13X-RAY DIFFRACTION13chain 'A' and (resid 75 through 86 )A75 - 86
14X-RAY DIFFRACTION14chain 'A' and (resid 87 through 103 )A87 - 103
15X-RAY DIFFRACTION15chain 'A' and (resid 104 through 116 )A104 - 116
16X-RAY DIFFRACTION16chain 'A' and (resid 117 through 126 )A117 - 126
17X-RAY DIFFRACTION17chain 'A' and (resid 127 through 137 )A127 - 137
18X-RAY DIFFRACTION18chain 'A' and (resid 138 through 151 )A138 - 151
19X-RAY DIFFRACTION19chain 'A' and (resid 152 through 166 )A152 - 166

+
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