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- PDB-3ddc: Crystal Structure of NORE1A in Complex with RAS -

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Basic information

Entry
Database: PDB / ID: 3ddc
TitleCrystal Structure of NORE1A in Complex with RAS
Components
  • GTPase HRas
  • Ras association domain-containing family protein 5
KeywordsHYDROLASE/APOPTOSIS / Oncogene / Tumorsuppressor / Ubiquitin Fold / RAS effector / RAP1 / H-RAS / RASSF1 / RASSF5 / RAPL / NORE1 / GMPPNP / Adaptor / Apoptosis / Microtubules / HYDROLASE-APOPTOSIS COMPLEX / Disease mutation / Golgi apparatus / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Palmitate / Prenylation / Proto-oncogene / Anti-oncogene / Cell cycle / Metal-binding / Microtubule / Phorbol-ester binding / Zinc-finger
Function / homology
Function and homology information


negative regulation of lymphocyte proliferation / lymphocyte proliferation / regulation of protein localization to nucleus / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / T-helper 1 type immune response / positive regulation of wound healing ...negative regulation of lymphocyte proliferation / lymphocyte proliferation / regulation of protein localization to nucleus / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / 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 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Schwann cell development / 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 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / 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 / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / 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 / intrinsic apoptotic signaling pathway / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / positive regulation of protein ubiquitination / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / positive regulation of MAP kinase activity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / Regulation of RAS by GAPs / endocytosis / Negative regulation of MAPK pathway / RAS processing / 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 / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions
Similarity search - Function
Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / SARAH domain / SARAH domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Phorbol esters/diacylglycerol binding domain (C1 domain) ...Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / SARAH domain / SARAH domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / Ras association domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStieglitz, B. / Bee, C. / Schwarz, D. / Yildiz, O. / Moshnikova, A. / Khokhlatchev, A. / Herrmann, C.
CitationJournal: Embo J. / Year: 2008
Title: Novel type of Ras effector interaction established between tumour suppressor NORE1A and Ras switch II
Authors: Stieglitz, B. / Bee, C. / Schwarz, D. / Yildiz, O. / Moshnikova, A. / Khokhlatchev, A. / Herrmann, C.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 20, 2011Group: Refinement description
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: Ras association domain-containing family protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8844
Polymers37,3382
Non-polymers5472
Water2,072115
1
A: GTPase HRas
B: Ras association domain-containing family protein 5
hetero molecules

A: GTPase HRas
B: Ras association domain-containing family protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7688
Polymers74,6754
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8420 Å2
ΔGint-48 kcal/mol
Surface area26570 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-20 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.600, 88.000, 56.500
Angle α, β, γ (deg.)90.00, 125.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18889.283 Da / Num. of mol.: 1 / Fragment: UNP residues 1-166 / Mutation: D30E, E31K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: PTAC / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P01112, small monomeric GTPase
#2: Protein Ras association domain-containing family protein 5 / New ras effector 1 / Regulator for cell adhesion and polarization enriched in lymphoid tissues / ...New ras effector 1 / Regulator for cell adhesion and polarization enriched in lymphoid tissues / RAPL / Effector protein NORE1A


Mass: 18448.352 Da / Num. of mol.: 1 / Fragment: RAS BINDING DOMAIN, UNP RESIDUES 200-358 / Mutation: L285M, K302D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rassf5, Nore1, Rapl / Plasmid: PGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5EBH1
#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


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100MM C2H3NAO2, 20% PEG 2000, 250MM (NH4)2SO4, 10MM DTE, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.78→19.59 Å / Num. obs: 29894 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.52 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.64
Reflection shellResolution: 1.78→1.85 Å / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 4.1 / % possible all: 86.3

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5P21

5p21


Resolution: 1.8→19.59 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.765 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1466 5 %RANDOM
Rwork0.193 ---
obs0.195 29320 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.03 Å2
2--0.05 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 33 115 2542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222469
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9873338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64624.298114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95815452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8461516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021814
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21044
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21679
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0411.51530
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70922413
X-RAY DIFFRACTIONr_scbond_it2.6131059
X-RAY DIFFRACTIONr_scangle_it4.0014.5925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 100 -
Rwork0.232 1912 -
obs--100 %
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)
11.3488-0.64260.57490.5121-0.13750.41810.00170.0375-0.0313-0.0026-0.01010.00880.0586-0.0820.0083-0.0088-0.0096-0.0008-0.0227-0.0066-0.01918.18729.77914.838
20.4639-0.1170.17930.4517-0.48771.0356-0.01230.05390.03520.0559-0.0721-0.0696-0.07980.08990.0844-0.01490.00320.0002-0.02130.0336-0.003825.41744.7230.082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B200 - 247
2X-RAY DIFFRACTION1B274 - 356
3X-RAY DIFFRACTION2A1 - 166

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