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- PDB-4wwq: Apo structure of the Grb7 SH2 domain -

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Basic information

Entry
Database: PDB / ID: 4wwq
TitleApo structure of the Grb7 SH2 domain
ComponentsGrowth factor receptor-bound protein 7
KeywordsSIGNALING PROTEIN / src Homology Domain / phosphotyrosine binding pocket
Function / homology
Function and homology information


GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / stress granule assembly / Tie2 Signaling / phosphatidylinositol binding / Downstream signal transduction / cell projection / epidermal growth factor receptor signaling pathway / Signaling by SCF-KIT ...GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / stress granule assembly / Tie2 Signaling / phosphatidylinositol binding / Downstream signal transduction / cell projection / epidermal growth factor receptor signaling pathway / Signaling by SCF-KIT / cytoplasmic stress granule / negative regulation of translation / positive regulation of cell migration / focal adhesion / protein kinase binding / RNA binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Growth factor receptor-bound protein 7 / : / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...Growth factor receptor-bound protein 7 / : / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / SH2 domain / SHC Adaptor Protein / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / Growth factor receptor-bound protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsWatson, G.M. / Ambaye, N.D. / Wilce, M.C. / Wilce, J.A.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Cyclic Peptides Incorporating Phosphotyrosine Mimetics as Potent and Specific Inhibitors of the Grb7 Breast Cancer Target.
Authors: Watson, G.M. / Gunzburg, M.J. / Ambaye, N.D. / Lucas, W.A. / Traore, D.A. / Kulkarni, K. / Cergol, K.M. / Payne, R.J. / Panjikar, S. / Pero, S.C. / Perlmutter, P. / Wilce, M.C. / Wilce, J.A.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4853
Polymers27,3812
Non-polymers1041
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-10 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.000, 84.000, 75.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
Detailsbiological unit is the same as asym.

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Components

#1: Protein Growth factor receptor-bound protein 7 / B47 / Epidermal growth factor receptor GRB-7 / GRB7 adapter protein


Mass: 13690.711 Da / Num. of mol.: 2 / Fragment: SH2 domain residues 438-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14451
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1 M sodium malonate, 0.1 M HEPES pH 7.0, 0.5%(v/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.8→27.495 Å / Num. all: 28306 / Num. obs: 28306 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 16.39 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Rsym value: 0.106 / Net I/av σ(I): 5.726 / Net I/σ(I): 16.7 / Num. measured all: 318795
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.911.30.5491.44643141250.1710.5494.9100
1.9-2.0111.30.3642.14364438720.1130.3647.2100
2.01-2.1511.30.2413.24159636790.0750.24110.6100
2.15-2.3211.30.184.23858334080.0560.1813.7100
2.32-2.5511.30.145.43558131440.0440.1416.6100
2.55-2.8511.30.1116.63213228330.0340.11120.2100
2.85-3.2911.30.0778.82856725250.0240.07725.8100
3.29-4.0211.30.0619.72411621420.0190.06134.3100
4.02-5.6911.10.05310.71834816480.0170.05336.9100
5.69-27.49510.50.05110.797979300.0160.05133.499.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementStarting model: 2QMS
Resolution: 1.8→27.495 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 1424 5.04 %
Rwork0.1691 26857 -
obs0.1705 28281 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.52 Å2 / Biso mean: 21.6853 Å2 / Biso min: 6.81 Å2
Refinement stepCycle: final / Resolution: 1.8→27.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 9 160 1988
Biso mean--16.67 28.62 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061863
X-RAY DIFFRACTIONf_angle_d1.1922515
X-RAY DIFFRACTIONf_chiral_restr0.049283
X-RAY DIFFRACTIONf_plane_restr0.005326
X-RAY DIFFRACTIONf_dihedral_angle_d12.028682
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A955X-RAY DIFFRACTION16.494TORSIONAL
12B955X-RAY DIFFRACTION16.494TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.86440.23171350.206827042839
1.8644-1.9390.22511380.186426442782
1.939-2.02730.21551430.178726922835
2.0273-2.13410.20891540.171426562810
2.1341-2.26780.20241470.169526802827
2.2678-2.44280.2081560.172826522808
2.4428-2.68840.19941600.177726682828
2.6884-3.0770.20281400.185826882828
3.077-3.87490.17851350.153426942829
3.8749-27.49860.1811160.153527792895
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.83531.8778-2.32987.0922-2.57043.6831-0.0128-0.28320.04920.16-0.2104-0.4731-0.0890.14590.18940.11980.012-0.02320.11020.0240.153532.190220.49264.7864
23.3382-0.00770.17552.6434-0.11383.4345-0.07960.1332-0.05760.0410.10580.30910.0127-0.2173-0.01890.104-0.00590.00810.0850.04630.116427.16885.95873.6098
35.2572-0.53680.67694.9772-0.58084.1441-0.05430.025-0.1166-0.0120.0138-0.10060.26990.1271-0.01880.09790.01810.03280.05090.01140.065640.10434.3018-3.158
42.3932-1.4284-0.88722.81443.35514.6634-0.00370.07940.0786-0.0473-0.18070.5559-0.2579-0.50120.13270.17350.0173-0.0160.15750.0480.176626.898912.6215-2.7233
58.6936-1.7880.06511.80481.01630.78870.19090.2189-0.2689-0.4278-0.1794-0.15110.03560.11760.0070.24130.0511-0.01160.17270.05730.202829.875514.6917-23.4385
62.69030.02390.26082.02320.16892.44830.0651-0.0601-0.03580.0113-0.0014-0.00630.07170.0804-0.04120.07990.0226-0.02670.09690.01270.086623.300426.328-17.4996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 421 through 437 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 438 through 487 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 488 through 518 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 519 through 532 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 414 through 448 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 449 through 532 )B0

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