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- PDB-3t6a: Structure of the C-terminal domain of BCAR3 -

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Basic information

Entry
Database: PDB / ID: 3t6a
TitleStructure of the C-terminal domain of BCAR3
ComponentsBreast cancer anti-estrogen resistance protein 3
KeywordsSIGNALING PROTEIN / Cdc25-homology domain / GTPase exchange factor
Function / homology
Function and homology information


endothelin receptor signaling pathway / lens morphogenesis in camera-type eye / response to xenobiotic stimulus => GO:0009410 / small GTPase-mediated signal transduction / phosphotyrosine residue binding / guanyl-nucleotide exchange factor activity / positive regulation of DNA replication / positive regulation of GTPase activity / kinase binding / insulin receptor signaling pathway ...endothelin receptor signaling pathway / lens morphogenesis in camera-type eye / response to xenobiotic stimulus => GO:0009410 / small GTPase-mediated signal transduction / phosphotyrosine residue binding / guanyl-nucleotide exchange factor activity / positive regulation of DNA replication / positive regulation of GTPase activity / kinase binding / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / positive regulation of MAPK cascade / focal adhesion / signal transduction / cytoplasm
Similarity search - Function
Breast cancer anti-estrogen resistance protein 3 / 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 / SH2 domain ...Breast cancer anti-estrogen resistance protein 3 / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-POG / Breast cancer anti-estrogen resistance protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Breast cancer anti-estrogen resistance protein 3
B: Breast cancer anti-estrogen resistance protein 3
C: Breast cancer anti-estrogen resistance protein 3
D: Breast cancer anti-estrogen resistance protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,88814
Polymers152,0394
Non-polymers84910
Water6,720373
1
A: Breast cancer anti-estrogen resistance protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4342
Polymers38,0101
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Breast cancer anti-estrogen resistance protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4342
Polymers38,0101
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Breast cancer anti-estrogen resistance protein 3


Theoretical massNumber of molelcules
Total (without water)38,0101
Polymers38,0101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Breast cancer anti-estrogen resistance protein 3


Theoretical massNumber of molelcules
Total (without water)38,0109
Polymers38,0101
Non-polymers08
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Breast cancer anti-estrogen resistance protein 3
B: Breast cancer anti-estrogen resistance protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8694
Polymers76,0202
Non-polymers8492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-12 kcal/mol
Surface area26930 Å2
MethodPISA
6
C: Breast cancer anti-estrogen resistance protein 3
D: Breast cancer anti-estrogen resistance protein 3


Theoretical massNumber of molelcules
Total (without water)76,02010
Polymers76,0202
Non-polymers08
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-19 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.233, 151.889, 196.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Breast cancer anti-estrogen resistance protein 3 / Novel SH2-containing protein 2 / SH2 domain-containing protein 3B


Mass: 38009.824 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 502-825) / Mutation: M536L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAR3, NSP2, SH2D3B, UNQ271/PRO308 / Production host: Escherichia coli (E. coli) / References: UniProt: O75815
#2: Chemical ChemComp-POG / (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL / POLYPROPYLENE GLYCOL / HEPTAPROPYLENE GLYCOL / Polypropylene glycol


Mass: 424.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H44O8
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPOLYPROPYLENE GLYCOL P 400 WAS PRESENT DURING CRYSTALLIZATION AND MODELED AS TWO POG MOLECULES IN ...POLYPROPYLENE GLYCOL P 400 WAS PRESENT DURING CRYSTALLIZATION AND MODELED AS TWO POG MOLECULES IN THE STRUCTURE. THESE APPEAR TO BE PRESENT AS THE TWO DIFFERENT STEREOISOMERS OF POLYPROPLENE GLYCOL.

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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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 15-20 % PEG3350, 0.04 M citric acid and 0.06 M Bis-Tris propane (pH 6.4), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→19.75 Å / Num. obs: 59059 / % possible obs: 98.7 % / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.761 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 24.59 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2442 2805 4.98 %
Rwork0.1736 --
obs0.1772 56380 94.27 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.279 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6322 Å2-0 Å20 Å2
2---7.2727 Å20 Å2
3---7.9049 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9792 0 41 373 10206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810046
X-RAY DIFFRACTIONf_angle_d1.05313572
X-RAY DIFFRACTIONf_dihedral_angle_d16.5313910
X-RAY DIFFRACTIONf_chiral_restr0.0691550
X-RAY DIFFRACTIONf_plane_restr0.0051754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48560.30512600.23174741X-RAY DIFFRACTION85
2.4856-2.5850.3352370.21574913X-RAY DIFFRACTION88
2.585-2.70230.31992770.21915061X-RAY DIFFRACTION90
2.7023-2.84440.30152780.21515173X-RAY DIFFRACTION92
2.8444-3.0220.30092760.20425353X-RAY DIFFRACTION95
3.022-3.25440.25342650.19045467X-RAY DIFFRACTION96
3.2544-3.58020.2683080.17975581X-RAY DIFFRACTION98
3.5802-4.09420.2322940.15565635X-RAY DIFFRACTION99
4.0942-5.14320.17713230.12465693X-RAY DIFFRACTION99
5.1432-19.76160.20052870.15815958X-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)
10.34810.0039-0.11070.69550.2670.8759-0.0030.06010.08290.73970.16750.80990.1622-0.49110.00490.37820.04340.31410.15030.06010.22673.924348.8158113.5986
20.1310.15480.18311.3737-0.17960.46220.0264-0.02990.01510.29790.01690.1007-0.17180.0334-0.04490.11610.0320.05930.0484-0.00570.095216.460656.2819103.6582
30.3804-0.15710.05661.4046-0.15830.5399-0.03960.0126-0.0840.45430.12620.2652-0.2279-0.0768-0.07660.24110.0390.12730.0709-0.00880.111711.46557.5749107.7736
40.7079-0.05750.54030.7740.04731.2465-0.0349-0.13870.08320.61210.2173-0.34730.31130.0832-0.14370.4160.0506-0.1410.1998-0.06170.169133.2499103.3612115.5439
50.3417-0.1655-0.00481.47740.36190.6274-0.05380.0253-0.00140.30120.03580.12640.06730.02850.02320.13480.0224-0.00970.05670.00270.069822.424295.7305104.0364
60.5851-0.25580.34581.22440.07911.0893-0.11720.0579-0.04050.44420.1505-0.15160.320.1573-0.06790.2190.0419-0.03670.0250.01470.022626.815994.4178108.8356
70.9095-0.23430.27070.72360.16580.67960.14910.221-0.5244-0.2566-0.0590.02550.0967-0.03260.41920.15380.03510.00310.168-0.17150.313110.54446.888954.4781
80.74060.57960.27750.91760.41560.5886-0.0117-0.1485-0.0544-0.1401-0.05950.1569-0.0395-0.05570.070.0480.0346-0.0310.0862-0.040.12748.284660.659765.1362
90.50530.3431-0.24530.34920.13720.8849-0.08570.0557-0.0878-0.07070.0179-0.0016-0.06360.13160.0630.06160.0267-0.00920.0627-0.0190.101212.448457.951760.8482
100.6664-0.24850.03650.9578-1.15181.5968-0.32090.46290.3737-0.77390.23490.07520.171-0.06370.08080.3549-0.0115-0.06970.33780.17730.378128.1815105.126750.4441
110.7741.4382-0.41922.795-1.11330.909-0.0505-0.1091-0.1486-0.2478-0.1223-0.37360.0670.0840.18320.03740.04230.05180.09750.03720.118334.175892.651965.9897
120.88760.7587-0.13091.4542-0.65540.3764-0.16680.12780.0504-0.34370.1126-0.07930.1893-0.10560.05010.148-0.01120.01910.09470.00580.013729.631594.225261.7754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 511:558)
2X-RAY DIFFRACTION2(chain A and resid 559:734)
3X-RAY DIFFRACTION3(chain A and resid 735:818)
4X-RAY DIFFRACTION4(chain B and resid 511:558)
5X-RAY DIFFRACTION5(chain B and resid 559:734)
6X-RAY DIFFRACTION6(chain B and resid 735:818)
7X-RAY DIFFRACTION7(chain C and resid 511:558)
8X-RAY DIFFRACTION8(chain C and resid 559:734)
9X-RAY DIFFRACTION9(chain C and resid 735:818)
10X-RAY DIFFRACTION10(chain D and resid 511:541)
11X-RAY DIFFRACTION11(chain D and resid 542:734)
12X-RAY DIFFRACTION12(chain D and resid 735:818)

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