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- PDB-1nvv: Structural evidence for feedback activation by RasGTP of the Ras-... -

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Entry
Database: PDB / ID: 1nvv
TitleStructural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS
Components
  • (Transforming protein p21/H-RAS- ...) x 2
  • Son of sevenless protein homolog 1
KeywordsSIGNALING PROTEIN / Proto-oncogene / GTP-binding / Guanine-nucleotide releasing factor
Function / homology
Function and homology information


midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / phospholipase C activator activity / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / phospholipase C activator activity / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling / positive regulation of small GTPase mediated signal transduction / oncogene-induced cell senescence / Activation of RAC1 / blood vessel morphogenesis / positive regulation of miRNA metabolic process / Signaling by LTK / positive regulation of ruffle assembly / epidermal growth factor receptor binding / T-helper 1 type immune response / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / leukocyte migration / NRAGE signals death through JNK / positive regulation of wound healing / defense response to protozoan / neurotrophin TRK receptor signaling pathway / Fc-epsilon receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / eyelid development in camera-type eye / GRB2:SOS provides linkage to MAPK signaling for Integrins / roof of mouth development / regulation of T cell proliferation / B cell homeostasis / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RET signaling / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / fibroblast growth factor receptor signaling pathway / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / positive regulation of protein targeting to membrane / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / Interleukin receptor SHC signaling / hair follicle development / adipose tissue development / Signalling to RAS / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / 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 FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / Signaling by FGFR2 in disease / RAC1 GTPase cycle / myelination / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / FCERI mediated Ca+2 mobilization / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / Downstream signal transduction / insulin-like growth factor receptor signaling pathway / Insulin receptor signalling cascade / GTPase activator activity / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / guanyl-nucleotide exchange factor activity / T cell activation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants
Similarity search - Function
Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / 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 ...Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / 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 / : / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Histone-fold / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / PHOSPHATE ION / GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 Å
AuthorsMargarit, S.M. / Sondermann, H. / Hall, B.E. / Nagar, B. / Hoelz, A. / Pirruccello, M. / Bar-Sagi, D. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS
Authors: Margarit, S.M. / Sondermann, H. / Hall, B.E. / Nagar, B. / Hoelz, A. / Pirruccello, M. / Bar-Sagi, D. / Kuriyan, J.
History
DepositionFeb 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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.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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: Transforming protein p21/H-RAS-1
R: Transforming protein p21/H-RAS-1
S: Son of sevenless protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,21210
Polymers94,1913
Non-polymers1,0217
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-58 kcal/mol
Surface area36480 Å2
MethodPISA
2
Q: Transforming protein p21/H-RAS-1
R: Transforming protein p21/H-RAS-1
S: Son of sevenless protein homolog 1
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)761,69980
Polymers753,52824
Non-polymers8,17156
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area100180 Å2
ΔGint-526 kcal/mol
Surface area260130 Å2
MethodPISA
3
Q: Transforming protein p21/H-RAS-1
R: Transforming protein p21/H-RAS-1
S: Son of sevenless protein homolog 1
hetero molecules

Q: Transforming protein p21/H-RAS-1
R: Transforming protein p21/H-RAS-1
S: Son of sevenless protein homolog 1
hetero molecules

Q: Transforming protein p21/H-RAS-1
R: Transforming protein p21/H-RAS-1
S: Son of sevenless protein homolog 1
hetero molecules

Q: Transforming protein p21/H-RAS-1
R: Transforming protein p21/H-RAS-1
S: Son of sevenless protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,84940
Polymers376,76412
Non-polymers4,08528
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area43610 Å2
ΔGint-270 kcal/mol
Surface area136550 Å2
MethodPISA
4
Q: Transforming protein p21/H-RAS-1
R: Transforming protein p21/H-RAS-1
S: Son of sevenless protein homolog 1
hetero molecules

Q: Transforming protein p21/H-RAS-1
R: Transforming protein p21/H-RAS-1
S: Son of sevenless protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,42520
Polymers188,3826
Non-polymers2,04314
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area18540 Å2
ΔGint-118 kcal/mol
Surface area71530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.163, 184.163, 179.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsTwo molecules of Ras bound to one molecule of Sos, one at the active site (chainID, R) and the other at a distal site (chainID, Q). The distal Ras has GTP bound to it, while the active site Ras is nucleotide-free.

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Components

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Transforming protein p21/H-RAS- ... , 2 types, 2 molecules QR

#1: Protein Transforming protein p21/H-RAS-1 / C-H-RAS


Mass: 18783.096 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166 / Mutation: Y64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS OR HRAS1 / Plasmid: p-ProEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01112
#2: Protein Transforming protein p21/H-RAS-1 / C-H-RAS


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS OR HRAS1 / Plasmid: p-ProEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01112

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Protein , 1 types, 1 molecules S

#3: Protein Son of sevenless protein homolog 1 / SOS-1


Mass: 56532.730 Da / Num. of mol.: 1
Fragment: residues 566-1046, including RAS GUANINE NUCLEOTIDE EXCHANGE FACTOR FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Plasmid: p-ProEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07889

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Non-polymers , 4 types, 322 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2-1.5 M phosphate, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
21.2-1.5 Mphosphate1reservoir
3100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2002 / Details: mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.18→64.19 Å / Num. all: 74722 / Num. obs: 74722 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.103 / Net I/σ(I): 13
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 6315 / Rsym value: 0.352 / % possible all: 81.9
Reflection
*PLUS
Lowest resolution: 64 Å / Num. measured all: 329000 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 81.9 % / Rmerge(I) obs: 0.352

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NVU

1nvu


Resolution: 2.18→64.19 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 5164 7.1 %RANDOM
Rwork0.208 ---
all0.208 72440 --
obs0.208 72440 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.8609 Å2 / ksol: 0.374455 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20 Å2
2--1.71 Å20 Å2
3----3.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.18→64.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 58 315 6908
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it2.622
X-RAY DIFFRACTIONc_scangle_it4.132.5
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 666 6.7 %
Rwork0.26 9201 -
obs-9201 75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2RASSOS_COMPLEXION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMRASSOS_COMPLEX
Refinement
*PLUS
Lowest resolution: 64 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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