[English] 日本語
Yorodumi
- PDB-7scx: KRAS full-length G12V in complex with RGL1 Ras association domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7scx
TitleKRAS full-length G12V in complex with RGL1 Ras association domain
Components
  • Isoform 2B of GTPase KRas
  • Ral guanine nucleotide dissociation stimulator-like 1
KeywordsONCOPROTEIN / GTPase / RalGEF / Complex / Domain-swap
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / small GTPase-mediated signal transduction / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis ...response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / small GTPase-mediated signal transduction / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / 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:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / p38MAPK events / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / homeostasis of number of cells within a tissue / Downstream signal transduction / GRB2 events in ERBB2 signaling / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / guanyl-nucleotide exchange factor activity / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / female pregnancy / RAF activation / Signaling by ERBB2 TMD/JMD mutants / Signaling by SCF-KIT / PPARA activates gene expression / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / visual learning / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Regulation of RAS by GAPs / Signaling by CSF1 (M-CSF) in myeloid cells / RAS processing / Negative regulation of MAPK pathway / 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 / GDP binding / Signaling by BRAF and RAF1 fusions / positive regulation of cellular senescence
Similarity search - Function
Ral guanine nucleotide dissociation stimulator-like 1 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal ...Ral guanine nucleotide dissociation stimulator-like 1 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Small GTPase, Ras-type / Small GTPase Ras domain 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 / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / PHOSPHATE ION / GTPase KRas / Ral guanine nucleotide dissociation stimulator-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsEves, B.J. / Kuntz, D.A. / Ikura, M. / Marshall, C.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structures of RGL1 RAS-Association Domain in Complex with KRAS and the Oncogenic G12V Mutant.
Authors: Eves, B.J. / Gebregiworgis, T. / Gasmi-Seabrook, G.M.C. / Kuntz, D.A. / Prive, G.G. / Marshall, C.B. / Ikura, M.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 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: Isoform 2B of GTPase KRas
B: Ral guanine nucleotide dissociation stimulator-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8395
Polymers32,1812
Non-polymers6593
Water2,126118
1
A: Isoform 2B of GTPase KRas
B: Ral guanine nucleotide dissociation stimulator-like 1
hetero molecules

A: Isoform 2B of GTPase KRas
B: Ral guanine nucleotide dissociation stimulator-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,67810
Polymers64,3614
Non-polymers1,3176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)121.950, 38.770, 68.240
Angle α, β, γ (deg.)90.000, 116.715, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21485.619 Da / Num. of mol.: 1 / Mutation: G12V
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
#2: Protein Ral guanine nucleotide dissociation stimulator-like 1 / RalGDS-like 1


Mass: 10695.026 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGL1, KIAA0959, RGL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZL6

-
Non-polymers , 4 types, 121 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M BIS-TRIS (pH 5.5), 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→33.86 Å / Num. obs: 20768 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 37.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.023 / Rpim(I) all: 0.023 / Rrim(I) all: 0.032 / Net I/av σ(I): 15.1 / Net I/σ(I): 15.1
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2049 / CC1/2: 0.8 / Rpim(I) all: 0.344 / Rrim(I) all: 0.487 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122+SVNrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LFD

1lfd


Resolution: 1.96→33.86 Å / SU ML: 0.2145 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 1025 4.94 %
Rwork0.1734 19735 -
obs0.1755 20760 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.3 Å2
Refinement stepCycle: LAST / Resolution: 1.96→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 38 118 2175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132113
X-RAY DIFFRACTIONf_angle_d1.15772865
X-RAY DIFFRACTIONf_chiral_restr0.0639324
X-RAY DIFFRACTIONf_plane_restr0.0083366
X-RAY DIFFRACTIONf_dihedral_angle_d6.3363297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.060.25061360.22612815X-RAY DIFFRACTION99.9
2.06-2.190.2751580.20062770X-RAY DIFFRACTION99.97
2.19-2.360.2481420.17972791X-RAY DIFFRACTION99.83
2.36-2.60.25531470.17392794X-RAY DIFFRACTION99.73
2.6-2.980.23561410.18332829X-RAY DIFFRACTION99.93
2.98-3.750.22641420.16682839X-RAY DIFFRACTION99.93
3.75-33.860.18171590.16482897X-RAY DIFFRACTION99.54
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)
10.1811759751230.1619257147260.04660475720860.1765266871540.009033677278990.220862407094-0.0102708706230.257741378892-0.076647326595-0.151188987826-0.3022828505270.696723212737-0.389258890463-0.1640894484070.0003700857965380.4838687393020.0783042891381-0.09866614035650.338680088918-0.03331882598130.461706714117-2.381789380641.082059134117.4906449113
20.592485465521-0.2327019532960.2712862208760.947773421748-0.07038918344661.2700373506-0.0999294591054-0.157879253560.1014411838050.2435683273890.0504503727856-0.0516260733936-0.282514621695-0.08408565940019.83102801306E-50.365703614932-0.00746132241563-0.01369670544440.322986763548-0.02921112441180.3711404585317.3243937964-2.0470834437126.6215523481
30.7201418248110.1694488030630.3770757508720.4015471138230.3873445163070.480086163523-0.0532258153271-0.0603076662646-0.155167553265-0.1290587061130.0538899114611-0.2325495231770.0121364165366-0.177541174856-9.91571088196E-60.447068852436-0.0139094055824-0.01191468510370.429314192318-0.01094292716320.463288470886-1.18487161862-7.9237560859620.502021982
40.517063358680.2462963855610.8561638637650.3840465421550.1699274572421.544699491830.1000011096990.24370696454-0.119833081725-0.211575199133-0.03769480342230.04853483036120.281440414967-0.01866432469220.0001181159595360.451530230622-0.00333302976327-0.009743834059670.35821900411-0.02779860243760.3706697923755.6030486971-12.559424525812.4505617026
51.07373279295-0.9022316800970.4165196866951.167488524840.4578824122721.77338223237-0.1081353490530.3786368923830.0950742863193-0.421749683431-0.0396260641738-0.0919075290513-0.2358689268050.31529712779-0.0001185373691820.456937371798-0.0407357599354-0.009174330959890.3779341121550.0288505293460.3674358110689.72512487518-2.5271062193810.4766460574
60.4228640514670.4165046418840.5957217982750.5176776821990.7552719805631.14293339828-0.0472259893159-0.2450341843050.08605997903030.4708691225160.03243704850970.479375871288-0.367093658016-0.601565392535-0.0004379160163550.419516267412-0.03695016721580.0649560893960.483090058390.01708234032940.394376383433-3.30104144172-9.2106691357436.6570207781
70.11693096117-0.0217167509012-0.02255731634070.0886576261031-0.05822019773450.04812903274390.0627005000808-0.5283399132950.2515704040240.2345672249120.18219328772-0.4705664204840.09465958474210.480618200848-0.0005007959399140.4738273256160.050448067592-0.03355273117440.5741720824180.05235617619810.4015181049211.50751863768-10.468777253843.8729229612
80.411440651755-0.3035755043060.2545907100790.876854272079-0.523517608560.321039797929-0.0654847530304-0.538282479440.803629124330.4924639326-0.140487697737-0.234875458425-0.7794067164880.0842959872997-0.01376612149690.565280531134-0.05072418043050.02504757470790.739117376875-0.06734550558910.506266140965-1.59096169556-3.7791323438144.6939421782
90.380235682972-0.01897075283750.402020443212.388580436390.1256414051870.4426014462550.35631354982-1.267006584170.04068016350570.515938203007-0.4570000252190.7448455724510.240950325705-0.631583551293-0.09319259005850.602594448629-0.07656553032140.1720702114610.9205693430460.01872226445820.562634309879-12.9120938137-11.178682540745.5548862102
100.639878310447-0.118173287252-0.3150163645390.1155964539330.07833082600260.266848439987-0.1420826245070.0724663691384-0.4109318759440.0600601720037-0.025326295507-0.045240874964-0.2410826351860.5140926936880.0005260124996740.544459236358-0.0136000598270.04494535779330.618498917740.07395804414390.475645829574-21.5136159489-7.6805823526525.7045630153
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 10 )AA1 - 101 - 10
22chain 'A' and (resid 11 through 46 )AA11 - 4611 - 46
33chain 'A' and (resid 47 through 73 )AA47 - 7347 - 73
44chain 'A' and (resid 74 through 104 )AA74 - 10474 - 104
55chain 'A' and (resid 105 through 169 )AA105 - 169105 - 169
66chain 'B' and (resid 683 through 709 )BF683 - 7091 - 27
77chain 'B' and (resid 710 through 720 )BF710 - 72028 - 38
88chain 'B' and (resid 721 through 738 )BF721 - 73839 - 56
99chain 'B' and (resid 739 through 754 )BF739 - 75457 - 72
1010chain 'B' and (resid 755 through 768 )BF755 - 76873 - 86

+
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