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- PDB-3t6g: Structure of the complex between NSP3 (SHEP1) and p130Cas -

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Basic information

Entry
Database: PDB / ID: 3t6g
TitleStructure of the complex between NSP3 (SHEP1) and p130Cas
Components
  • Breast cancer anti-estrogen resistance protein 1
  • SH2 domain-containing protein 3C
KeywordsSIGNALING PROTEIN / CELL ADHESION / Cdc25-homology domain / GTPase exchange factor / Focal-adhesion targeting domain
Function / homology
Function and homology information


antigen receptor-mediated signaling pathway / endothelin receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / cellular response to hepatocyte growth factor stimulus / small GTPase-mediated signal transduction / p130Cas linkage to MAPK signaling for integrins / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases ...antigen receptor-mediated signaling pathway / endothelin receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / cellular response to hepatocyte growth factor stimulus / small GTPase-mediated signal transduction / p130Cas linkage to MAPK signaling for integrins / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / JNK cascade / ruffle / cell chemotaxis / Downstream signal transduction / guanyl-nucleotide exchange factor activity / positive regulation of endothelial cell migration / actin filament organization / integrin-mediated signaling pathway / regulation of cell growth / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / ruffle membrane / SH3 domain binding / VEGFA-VEGFR2 Pathway / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / actin cytoskeleton / lamellipodium / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / T cell receptor signaling pathway / regulation of apoptotic process / cell adhesion / positive regulation of cell migration / G protein-coupled receptor signaling pathway / cell division / axon / focal adhesion / protein kinase binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / BCAR1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / Alpha-catenin/vinculin-like / Son of Sevenless (SoS) protein; Chain S, domain 2 ...: / BCAR1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / Alpha-catenin/vinculin-like / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Breast cancer anti-estrogen resistance protein 1 / SH2 domain-containing protein 3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsMace, P.D. / Robinson, H. / Riedl, S.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: NSP-Cas protein structures reveal a promiscuous interaction module in cell signaling.
Authors: Mace, P.D. / Wallez, Y. / Dobaczewska, M.K. / Lee, J.J. / Robinson, H. / Pasquale, E.B. / Riedl, S.J.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: SH2 domain-containing protein 3C
B: Breast cancer anti-estrogen resistance protein 1
C: SH2 domain-containing protein 3C
D: Breast cancer anti-estrogen resistance protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1565
Polymers125,0974
Non-polymers591
Water1,06359
1
A: SH2 domain-containing protein 3C
B: Breast cancer anti-estrogen resistance protein 1


Theoretical massNumber of molelcules
Total (without water)62,5482
Polymers62,5482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-14 kcal/mol
Surface area19590 Å2
MethodPISA
2
C: SH2 domain-containing protein 3C
D: Breast cancer anti-estrogen resistance protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6073
Polymers62,5482
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.883, 171.883, 78.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein SH2 domain-containing protein 3C / Novel SH2-containing protein 3


Mass: 37003.707 Da / Num. of mol.: 2 / Fragment: UNP residues 539-860 / Mutation: C654S, C755S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH2D3C, NSP3, UNQ272/PRO309/PRO34088 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N5H7
#2: Protein Breast cancer anti-estrogen resistance protein 1 / CRK-associated substrate / Cas scaffolding protein family member 1 / p130cas


Mass: 25544.709 Da / Num. of mol.: 2 / Fragment: UNP residues 645-870
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAR1, CAS, CASS1, CRKAS / Production host: Escherichia coli (E. coli) / References: UniProt: P56945
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: PEG3350 and sodium citrate (pH 7.8), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorDate: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→29.5 Å / Num. obs: 39585 / % possible obs: 99.8 % / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→29.555 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 31.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2658 1871 5.02 %
Rwork0.1966 --
obs0.1999 37296 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.968 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.3128 Å2-0 Å20 Å2
2---11.3128 Å20 Å2
3---22.6255 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 4 59 6590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086649
X-RAY DIFFRACTIONf_angle_d1.0768996
X-RAY DIFFRACTIONf_dihedral_angle_d16.1042458
X-RAY DIFFRACTIONf_chiral_restr0.0681070
X-RAY DIFFRACTIONf_plane_restr0.0051140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58940.41331780.29753081X-RAY DIFFRACTION83
2.5894-2.6930.32911690.26493234X-RAY DIFFRACTION86
2.693-2.81550.31031720.23463395X-RAY DIFFRACTION90
2.8155-2.96380.31711860.23233457X-RAY DIFFRACTION93
2.9638-3.14930.36751880.23993558X-RAY DIFFRACTION95
3.1493-3.39210.31092000.2293643X-RAY DIFFRACTION97
3.3921-3.73290.25711970.21173709X-RAY DIFFRACTION99
3.7329-4.27170.24461940.17793750X-RAY DIFFRACTION99
4.2717-5.37650.21491910.15983782X-RAY DIFFRACTION100
5.3765-29.5570.24981960.18353816X-RAY DIFFRACTION99
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)
13.20631.26810.66962.54421.32012.71680.1078-0.11570.1215-0.00590.0724-0.1938-0.15480.0391-0.11260.16340.009-0.06860.28370.12950.255965.155280.211617.1066
21.6977-0.35710.13385.97071.50830.4329-0.10550.4592-0.0581-1.4832-0.39730.0541-0.5040.5770.33020.41060.0313-0.1180.49370.0230.177854.260678.52436.9184
31.99730.83091.43612.5580.46293.66320.0392-0.2362-0.12510.09660.007-0.06170.1162-0.0473-0.07230.2551-0.0667-0.07290.40450.07050.376161.378978.705318.7765
42.0759-0.0333-1.60082.45660.4762.06710.31780.8798-0.3149-0.88480.2913-0.93860.12910.7147-0.38860.8303-0.23410.35051.3451-0.76690.934694.079557.4603-15.0256
51.7062-0.2770.07820.26941.0073.007-0.09420.8435-1.2671-0.11850.4657-0.06190.18260.3943-0.28060.4187-0.14960.11970.7256-0.50170.878982.283656.8679-5.3411
63.1001-0.57450.35911.32990.6820.66970.21980.2426-1.60910.5051-1.10691.2603-0.1064-1.29680.9140.59110.04060.17070.8555-0.44311.598796.881749.08528.2019
70.1291-0.1290.47421.3564-0.30832.0814-0.18491.1844-0.4299-0.05540.7397-0.8978-0.08480.5807-0.54330.6596-0.21390.33591.5155-0.71231.142992.996362.4737-14.4779
87.65991.0748-0.2914.37461.22139.04870.3704-0.0266-0.603-0.8047-0.8271.47211.77040.24160.24490.69020.1869-0.02230.42480.2360.796139.715957.124310.503
92.34830.1717-0.09951.2668-0.36382.0297-0.1037-0.0982-0.21870.0349-0.06260.4693-0.0245-0.05850.12460.2940.0084-0.19130.39-0.05430.52532.001475.51415.3231
100.571.14250.56949.94023.16315.29650.1954-0.0992-0.33150.0347-1.1751.46090.4964-0.97520.77820.4478-0.0229-0.08040.4671-0.05670.730232.396955.27463.9824
110.465-1.2915-0.09863.65320.87793.4027-0.31682.61590.12690.1709-2.44860.16390.4928-0.55562.38530.20780.05650.34341.5296-0.32732.4384119.020746.22321.0954
121.4341-0.4567-0.3071.42350.73691.3128-0.03160.1798-1.9343-0.20870.0955-1.1480.27270.9335-0.14340.22810.13840.06730.6204-0.08621.772107.278147.281416.3702
130.10840.2831-0.39190.6277-0.88141.2151-0.4349-0.6328-1.0803-0.1638-0.5478-1.3258-0.1041.19230.90140.4072-0.01840.17831.113-0.49673.1218122.973738.00376.7509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 543:732)
2X-RAY DIFFRACTION2(chain A and resid 733:769)
3X-RAY DIFFRACTION3(chain A and resid 770:855)
4X-RAY DIFFRACTION4(chain C and resid 569:661)
5X-RAY DIFFRACTION5(chain C and resid 662:755)
6X-RAY DIFFRACTION6(chain C and resid 757:785)
7X-RAY DIFFRACTION7(chain C and resid 786:855)
8X-RAY DIFFRACTION8(chain B and resid 738:755)
9X-RAY DIFFRACTION9(chain B and resid 756:857)
10X-RAY DIFFRACTION10(chain B and resid 858:872)
11X-RAY DIFFRACTION11(chain D and resid 742:755)
12X-RAY DIFFRACTION12(chain D and resid 756:858)
13X-RAY DIFFRACTION13(chain D and resid 859:872)

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