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- PDB-6v65: Crystal structure of KRAS(GMPPNP)-NF1(GRD)-SPRED1 complex -

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Basic information

Entry
Database: PDB / ID: 6v65
TitleCrystal structure of KRAS(GMPPNP)-NF1(GRD)-SPRED1 complex
Components
  • GTPase KRas
  • Neurofibromin
  • Sprouty-related, EVH1 domain-containing protein 1
KeywordsONCOPROTEIN / Neurofibromin / RAS / Legius syndrome / RasGAP / GAP / SPRED / K-Ras / EVH1 / GRD
Function / homology
Function and homology information


negative regulation of lens fiber cell differentiation / stem cell factor receptor binding / negative regulation of intracellular signal transduction / FGFRL1 modulation of FGFR1 signaling / positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / negative regulation of Schwann cell migration / Schwann cell migration ...negative regulation of lens fiber cell differentiation / stem cell factor receptor binding / negative regulation of intracellular signal transduction / FGFRL1 modulation of FGFR1 signaling / positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / negative regulation of Schwann cell migration / Schwann cell migration / amygdala development / vascular associated smooth muscle cell migration / Schwann cell proliferation / negative regulation of mast cell proliferation / vasculogenesis involved in coronary vascular morphogenesis / mast cell apoptotic process / gamma-aminobutyric acid secretion, neurotransmission / vascular associated smooth muscle cell proliferation / negative regulation of Schwann cell proliferation / glutamate secretion, neurotransmission / negative regulation of leukocyte migration / mast cell proliferation / forebrain morphogenesis / regulation of cell-matrix adhesion / hair follicle maturation / regulation of blood vessel endothelial cell migration / camera-type eye morphogenesis / cell communication / smooth muscle tissue development / negative regulation of neurotransmitter secretion / negative regulation of oligodendrocyte differentiation / sympathetic nervous system development / myeloid leukocyte migration / peripheral nervous system development / negative regulation of cell migration involved in sprouting angiogenesis / phosphatidylcholine binding / myelination in peripheral nervous system / negative regulation of Ras protein signal transduction / metanephros development / phosphatidylethanolamine binding / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / collagen fibril organization / regulation of long-term synaptic potentiation / regulation of postsynapse organization / endothelial cell proliferation / regulation of bone resorption / positive regulation of DNA damage response, signal transduction by p53 class mediator / artery morphogenesis / neural tube development / negative regulation of epithelial to mesenchymal transition / adrenal gland development / response to mineralocorticoid / negative regulation of neuroblast proliferation / GMP binding / forebrain astrocyte development / LRR domain binding / negative regulation of protein import into nucleus / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / spinal cord development / negative regulation of astrocyte differentiation / negative regulation of vascular associated smooth muscle cell migration / pigmentation / response to gravity / epithelial tube branching involved in lung morphogenesis / negative regulation of endothelial cell proliferation / negative regulation of osteoclast differentiation / type I pneumocyte differentiation / Rac protein signal transduction / regulation of MAPK cascade / oligodendrocyte differentiation / 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 / RAS signaling downstream of NF1 loss-of-function variants / skeletal muscle cell differentiation / RUNX3 regulates p14-ARF / negative regulation of cell-matrix adhesion / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway via death domain receptors / SOS-mediated signalling / positive regulation of GTPase activity / Activated NTRK3 signals through RAS / protein serine/threonine kinase inhibitor activity / Activated NTRK2 signals through RAS / neuroblast proliferation / SHC1 events in ERBB4 signaling / regulation of angiogenesis / cardiac muscle cell proliferation / Signalling to RAS / phosphatase binding / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / regulation of ERK1 and ERK2 cascade / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation
Similarity search - Function
c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / : / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site ...c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / : / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Divergent CRAL/TRIO domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase activation protein / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / PH-like domain superfamily / Armadillo-type fold / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas / Neurofibromin / Sprouty-related, EVH1 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.763 Å
AuthorsYan, W. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR.
Authors: Yan, W. / Markegard, E. / Dharmaiah, S. / Urisman, A. / Drew, M. / Esposito, D. / Scheffzek, K. / Nissley, D.V. / McCormick, F. / Simanshu, D.K.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sprouty-related, EVH1 domain-containing protein 1
B: Neurofibromin
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,54910
Polymers69,7533
Non-polymers7967
Water905
1
B: Neurofibromin
C: GTPase KRas
hetero molecules

A: Sprouty-related, EVH1 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,54910
Polymers69,7533
Non-polymers7967
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area4630 Å2
ΔGint-58 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.556, 70.553, 80.311
Angle α, β, γ (deg.)90.000, 99.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Sprouty-related, EVH1 domain-containing protein 1 / hSpred1


Mass: 12853.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPRED1 / Production host: unidentified baculovirus / References: UniProt: Q7Z699
#2: Protein Neurofibromin / Neurofibromatosis-related protein NF-1


Mass: 37570.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21359
#3: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19328.811 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

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Non-polymers , 5 types, 12 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: 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
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 100 mM Tris pH7.8 100 mM ammonium sulfate 300 mM sodium formate 3% PEG3350, 3.5% PGA-LM 10% detergent ANAPOE-80

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.76→52.677 Å / Num. obs: 20234 / % possible obs: 97.6 % / Redundancy: 4.346 % / Biso Wilson estimate: 75.724 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.083 / Χ2: 0.929 / Net I/σ(I): 11.7 / Num. measured all: 87931
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.76-2.934.2790.6242.0213514331831580.8730.70995.2
2.93-3.134.3240.3333.6913353313730880.9590.37998.4
3.13-3.384.5640.2055.9713313293029170.9840.23299.6
3.38-3.74.4560.1139.9511796266426470.9930.12899.4
3.7-4.144.2880.07314.4710318244824060.9960.08298.3
4.14-4.784.1590.055208606215320690.9970.06396.1
4.78-5.854.4660.05322.688029183817980.9970.0697.8
5.85-8.254.1940.04823.765742143013690.9970.05595.7
8.25-52.6774.1690.03632.832608247820.9970.04194.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OB2, 3SYX

6ob2

3syx


Resolution: 2.763→52.677 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1008 5 %
Rwork0.2206 19164 -
obs0.2216 20172 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.39 Å2 / Biso mean: 96.2587 Å2 / Biso min: 35.52 Å2
Refinement stepCycle: final / Resolution: 2.763→52.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 46 5 4606
Biso mean--71.47 80.58 -
Num. residues----578
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.763-2.90820.43181400.4123265694
2.9082-3.09030.38731430.3248271298
3.0903-3.32890.29361460.2876277599
3.3289-3.66380.28241460.2589278299
3.6638-4.19380.20871440.2022273598
4.1938-5.2830.21881430.1789273097
5.283-52.6770.19391460.1844277496
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)
10.4114-0.4330.06060.7773-0.42660.40750.6571-0.13360.40310.5247-0.2717-0.5040.2927-1.078101.0669-0.30710.33151.311-0.04291.263332.83630.5627-0.7086
20.1687-0.0074-0.15520.10470.0360.14550.8846-0.46691.1001-0.1891-1.05841.0179-1.01090.14170.00011.2985-0.12630.45421.3407-0.12541.369630.346238.8458.0496
30.1040.03680.13980.01230.05050.18780.32560.3634-0.45070.7721-0.2855-0.2311-0.0983-0.4273-00.8499-0.18760.11251.26790.15470.993938.876829.2636-9.7974
40.1854-0.14630.10550.3273-0.31180.28820.81980.741-1.1821-1.4541-0.0610.6325-0.331-0.79120.00161.13650.03690.12511.10630.11791.475245.56830.1849-12.7099
50.00880.0071-0.01010.0263-0.01980.0166-0.29320.2857-0.1210.4396-0.1840.1341-1.29570.33990.00011.1450.24280.22341.84170.71791.780825.353337.935-9.5643
60.19740.08680.15380.18290.20860.25740.09490.0746-0.00930.2849-0.13650.0894-0.351-0.210900.8743-0.04560.15021.3670.26781.124241.057329.56892.3499
70.1445-0.0780.10680.09110.03130.2353-0.0816-0.26960.25470.989-0.6318-0.73620.23190.6802-0.00011.0813-0.38850.25741.3725-0.05441.325240.555232.68216.4622
80.4407-0.08970.23110.391-0.45950.5679-0.1202-0.5738-1.09930.0049-0.83-0.03510.48370.33101.0838-0.07460.40981.27750.20331.381937.963923.9556-0.0228
91.79940.10660.72121.99461.26611.03740.2755-0.85230.15660.7774-0.22410.3688-0.57560.4745-01.0288-0.06980.21191.2164-0.01861.157819.066727.871617.2731
104.27880.8014-0.3832.91480.12771.3078-0.13710.6008-0.0315-0.30110.1002-0.07250.17640.131800.74010.0132-0.02790.8601-0.00260.63162.71966.51211.2233
110.0887-0.1037-0.07040.14820.12940.12010.6641-0.88930.46092.3775-0.16760.8705-0.6797-0.33130.00011.6495-0.40590.36681.4394-0.41761.638519.794943.960122.8676
120.91540.2911-0.77345.03952.37764.37040.0833-0.2904-0.0608-0.4907-0.47041.30741.3494-0.6638-0.40430.4970.067-0.22230.4580.11080.6845-11.59095.464435.9911
130.00080.00490.0072.3572.01211.72130.1353-0.37180.36380.7589-0.4032-0.07590.60280.3145-0.14290.44630.0812-0.10540.71170.10950.62263.10935.807835.2368
140.2608-0.10230.0110.14780.15480.2321.13880.0717-0.87110.99390.05510.4262-0.27861.352200.98360.05100.84970.0761.18657.52992.527131.4069
150.10790.0509-0.0790.1164-0.06340.06120.12940.0724-0.23640.8605-0.40090.3425-1.4394-1.5443-0.03460.96920.0248-0.07910.7352-0.00760.491-7.3237-0.332635.676
160.50520.0350.62060.40780.21030.83130.21870.0625-0.16420.8713-0.26260.4837-0.4641-0.555300.7967-0.00260.07650.57130.02680.6944-8.08834.250236.2594
170.195-0.2025-0.14120.24940.01780.4550.3210.2582-0.6938-0.7314-0.2074-0.2191-0.8616-0.144300.91750.1149-0.06640.74990.03220.7469-6.616714.958923.5179
180.24830.24960.33480.70450.22362.070.47690.14461.19610.0061-0.26550.2109-0.2316-0.023400.80330.01760.02960.63620.04570.7953-4.360419.611635.2998
190.165-0.16270.05290.1789-0.0890.0794-0.1317-1.19940.2249-0.28910.0186-1.2798-0.07380.61750.00140.9382-0.0868-0.15250.81730.02160.972212.52616.548943.4753
200.06290.0890.0850.12670.10050.19850.2214-0.1650.0110.2003-0.33150.51320.05790.1974-01.0032-0.0230.16590.7484-0.04850.982-0.430524.387246.2057
210.1845-0.2686-0.10250.41360.03320.4159-0.231-0.64440.5881.54840.1776-0.2712-0.0361-0.0946-0.00210.89370.0169-0.18210.6373-0.01530.67383.111610.437245.1037
220.64820.29570.17240.43810.31650.71140.9309-2.06020.86810.3099-0.3721.3953-0.2309-0.53340.00810.8329-0.00320.09620.81660.01811.0229-10.67838.924344.5963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 25 )A13 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 39 )A26 - 39
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 48 )A40 - 48
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 64 )A49 - 64
5X-RAY DIFFRACTION5chain 'A' and (resid 65 through 69 )A65 - 69
6X-RAY DIFFRACTION6chain 'A' and (resid 70 through 88 )A70 - 88
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 96 )A89 - 96
8X-RAY DIFFRACTION8chain 'A' and (resid 97 through 124 )A97 - 124
9X-RAY DIFFRACTION9chain 'B' and (resid 1205 through 1279 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1280 through 1485 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1486 through 1528 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 10 )C1 - 10
13X-RAY DIFFRACTION13chain 'C' and (resid 11 through 24 )C11 - 24
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 36 )C25 - 36
15X-RAY DIFFRACTION15chain 'C' and (resid 37 through 46 )C37 - 46
16X-RAY DIFFRACTION16chain 'C' and (resid 47 through 61 )C47 - 61
17X-RAY DIFFRACTION17chain 'C' and (resid 62 through 74 )C62 - 74
18X-RAY DIFFRACTION18chain 'C' and (resid 75 through 116 )C75 - 116
19X-RAY DIFFRACTION19chain 'C' and (resid 117 through 126 )C117 - 126
20X-RAY DIFFRACTION20chain 'C' and (resid 127 through 137 )C127 - 137
21X-RAY DIFFRACTION21chain 'C' and (resid 138 through 151 )C138 - 151
22X-RAY DIFFRACTION22chain 'C' and (resid 152 through 168 )C152 - 168

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