[English] 日本語
Yorodumi
- PDB-7vv8: Crystal Structure of HRasQ61L(GMPPNP-bound) in complex with the R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vv8
TitleCrystal Structure of HRasQ61L(GMPPNP-bound) in complex with the Ras-binding domain(RBD) of SIN1
Components
  • GTPase HRas
  • 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 / phospholipase C activator activity / negative regulation of Ras protein signal transduction / phosphatidylinositol-3,4-bisphosphate binding / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly ...TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / phospholipase C activator activity / negative regulation of Ras protein signal transduction / phosphatidylinositol-3,4-bisphosphate binding / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / phosphatidylinositol-3,5-bisphosphate binding / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Constitutive Signaling by AKT1 E17K in Cancer / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / phosphatidylinositol-3,4,5-trisphosphate binding / CD28 dependent PI3K/Akt signaling / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / cellular response to nutrient levels / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / cytoskeleton organization / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / phosphatidylinositol-4,5-bisphosphate binding / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / substantia nigra development / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / intrinsic apoptotic signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / positive regulation of GTPase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of epithelial cell proliferation / small monomeric GTPase / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / regulation of actin cytoskeleton organization / animal organ morphogenesis / FCERI mediated MAPK activation / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / positive regulation of MAP kinase activity / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / G protein activity / small GTPase binding / positive regulation of type II interferon production
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. / Rho (Ras homology) subfamily of Ras-like 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. / 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 HRas / 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 4, 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
A: GTPase HRas
C: Target of rapamycin complex 2 subunit MAPKAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3054
Polymers28,7582
Non-polymers5472
Water5,026279
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)101.316, 101.316, 124.291
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18947.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112, small monomeric GTPase
#2: 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: 9811.109 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
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG20000, 0.1M Sodim citrate. pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→26.49 Å / Num. obs: 41520 / % possible obs: 98.87 % / Redundancy: 16.5 % / Biso Wilson estimate: 19.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07592 / Net I/σ(I): 25.57
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 0.7526 / Num. unique obs: 4098 / CC1/2: 0.897 / % possible all: 99.78

-
Processing

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

4g0n


Resolution: 1.7→26.49 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 3746 4.82 %
Rwork0.1796 73910 -
obs-41497 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.43 Å2 / Biso mean: 27.1099 Å2 / Biso min: 8.19 Å2
Refinement stepCycle: final / Resolution: 1.7→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 33 279 2260
Biso mean--13.7 37.86 -
Num. residues----245
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.720.22611460.22532760100
1.72-1.740.25431520.21482726100
1.74-1.770.23191480.22022740100
1.77-1.790.23221290.2062275699
1.79-1.820.2071160.2052275199
1.82-1.850.26421170.2131274498
1.85-1.880.23661630.2038271699
1.88-1.910.2181520.185277099
1.91-1.950.22151620.1785271599
1.95-1.980.19951760.18022729100
1.98-2.020.22551210.17372771100
2.02-2.070.18291400.17182802100
2.07-2.120.22031250.17572745100
2.12-2.170.20481610.1742747100
2.17-2.230.24331390.17332752100
2.23-2.290.21911270.17212815100
2.29-2.370.16181450.17532730100
2.37-2.450.17521500.17792759100
2.45-2.550.19091680.18322734100
2.55-2.670.22331170.17182788100
2.67-2.810.18781420.18342752100
2.81-2.980.16831020.18112813100
2.98-3.210.17461430.1717271799
3.21-3.530.181340.165269397
3.53-4.040.17621250.1548266896
4.04-5.090.18941240.1489260594
5.09-26.490.20991220.1872261293
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)
15.68491.5865-2.32481.2164-1.03081.54610.14180.12340.1954-0.0378-0.0188-0.132-0.18150.3102-0.03710.1109-0.08150.00770.26460.02650.1652-18.154234.16117.2213
20.87740.22470.1040.29-0.07370.06320.1089-0.16380.20270.241-0.15010.0542-0.1720.0564-0.06960.159-0.2466-0.00450.21280.05130.1522-26.040436.777131.8865
33.4395-0.476-0.12070.60220.10190.47040.0188-0.01630.01760.0128-0.0807-0.0162-0.01380.29420.02840.1308-0.1016-0.01230.32810.04820.1639-17.74736.979221.6062
45.913-2.1759-3.5951.60591.5914.02550.0576-0.05760.1394-0.0315-0.07430.2846-0.1486-0.3007-0.00390.2547-0.0903-0.03550.41550.03020.2081-33.961933.820215.0015
50.72810.2696-0.94730.7085-0.98082.1279-0.04880.2617-0.1986-0.20310.04660.08750.2645-0.26890.01430.1747-0.1177-0.03150.2030.00230.1759-30.978423.515420.8484
60.6456-0.1877-1.53661.76883.26688.9154-0.00590.1371-0.1472-0.341-0.0494-0.0379-0.40650.09130.05990.1874-0.0628-0.01010.18650.01250.1554-23.652722.181617.4885
70.56440.02630.09020.85930.06510.76260.1594-0.1287-0.14240.214-0.1428-0.17960.19530.2954-0.01930.1516-0.0769-0.05160.20860.04970.1902-21.040321.412128.3774
84.9997-0.3528-0.95280.8113-0.11451.80530.00220.0641-0.18760.04830.00770.23630.102-0.22040.0070.1627-0.0875-0.03010.17190.02930.1819-33.670747.360218.9692
93.9519-0.2478-0.91841.82190.19161.53830.0476-0.17770.01360.14620.0125-0.0456-0.1156-0.0089-0.04810.1365-0.1028-0.00840.16610.02650.1489-28.899246.779822.3788
104.54052.23370.77182.21642.16843.27140.0009-0.12910.00940.1587-0.02280.1496-0.0816-0.2204-0.01860.2941-0.00830.09090.39210.00330.3281-42.539755.179125.6018
112.3256-1.39450.30973.5552-0.01882.191-0.0518-0.2863-0.00290.380.11110.0921-0.0187-0.0724-0.02290.3106-0.09520.01540.30420.00830.1542-29.456251.989629.1475
122.0831-0.46540.11162.0844-0.41062.1732-0.026-0.29370.02620.33720.1392-0.1798-0.03590.1249-0.01150.4178-0.1244-0.05510.24030.00830.1822-23.483657.797226.7733
132.26380.6615-0.45861.24880.07341.28230.0541-0.0850.25040.06630.00830.0507-0.2027-0.0382-0.08540.3868-0.0651-00.19240.00440.2245-29.949762.634719.7597
140.1504-0.5265-0.59936.26071.47713.78240.00960.01310.1660.0035-0.03870.2812-0.2048-0.2969-0.00370.2333-0.0099-0.00790.2347-0.00180.2392-38.582458.065917.8323
151.28731.844-0.42595.11951.54824.40350.09050.0592-0.24410.17870.0232-0.30110.00740.2398-0.13030.3054-0.0921-0.0320.18730.01330.1717-24.70955.414120.6323
163.69343.18073.86852.74973.33414.0520.00610.0592-0.01380.11610.0574-0.1528-0.05240.3382-0.10950.3106-0.0431-0.03980.3510.04690.3072-17.924759.906221.6258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 36 )A11 - 36
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 61 )A37 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 74 )A62 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 104 )A75 - 104
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 116 )A105 - 116
7X-RAY DIFFRACTION7chain 'A' and (resid 117 through 166 )A117 - 166
8X-RAY DIFFRACTION8chain 'C' and (resid 277 through 285 )C277 - 285
9X-RAY DIFFRACTION9chain 'C' and (resid 286 through 294 )C286 - 294
10X-RAY DIFFRACTION10chain 'C' and (resid 295 through 300 )C295 - 300
11X-RAY DIFFRACTION11chain 'C' and (resid 301 through 313 )C301 - 313
12X-RAY DIFFRACTION12chain 'C' and (resid 314 through 327 )C314 - 327
13X-RAY DIFFRACTION13chain 'C' and (resid 328 through 340 )C328 - 340
14X-RAY DIFFRACTION14chain 'C' and (resid 341 through 347 )C341 - 347
15X-RAY DIFFRACTION15chain 'C' and (resid 348 through 353 )C348 - 353
16X-RAY DIFFRACTION16chain 'C' and (resid 354 through 358 )C354 - 358

+
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