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- PDB-3pqz: Grb7 SH2 with peptide -

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Basic information

Entry
Database: PDB / ID: 3pqz
TitleGrb7 SH2 with peptide
Components
  • Growth factor receptor-bound protein 7
  • cyclic peptide
KeywordsPROTEIN BINDING / SH2 / binds phosphotyrosine / tyrosine kinases / cytoplasmic
Function / homology
Function and homology information


GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / Tie2 Signaling / stress granule assembly / phosphatidylinositol binding / Downstream signal transduction / cell projection / Signaling by SCF-KIT / epidermal growth factor receptor signaling pathway ...GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / Tie2 Signaling / stress granule assembly / phosphatidylinositol binding / Downstream signal transduction / cell projection / Signaling by SCF-KIT / epidermal growth factor receptor signaling pathway / 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 / RA like domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / 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 / RA like domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / 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
Growth factor receptor-bound protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.413 Å
AuthorsWilce, J.A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural basis of binding by cyclic nonphosphorylated Peptide antagonists of grb7 implicated in breast cancer progression
Authors: Ambaye, N.D. / Pero, S.C. / Gunzburg, M.J. / Yap, M. / Clayton, D.J. / Del Borgo, M.P. / Perlmutter, P. / Aguilar, M.I. / Shukla, G.S. / Peletskaya, E. / Cookson, M.M. / Krag, D.N. / Wilce, M.C. / Wilce, J.A.
History
DepositionNov 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
L: cyclic peptide
M: cyclic peptide


Theoretical massNumber of molelcules
Total (without water)56,6716
Polymers56,6716
Non-polymers00
Water1,856103
1
A: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
L: cyclic peptide


Theoretical massNumber of molelcules
Total (without water)28,3353
Polymers28,3353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Growth factor receptor-bound protein 7
C: Growth factor receptor-bound protein 7
M: cyclic peptide


Theoretical massNumber of molelcules
Total (without water)28,3353
Polymers28,3353
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.660, 79.110, 54.690
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13L
23M

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLNGLNchain A and (resseq 429:442 or resseq 444:461 or resseq...AA429 - 44214 - 27
121LEULEUGLNGLNchain A and (resseq 429:442 or resseq 444:461 or resseq...AA444 - 46129 - 46
131GLYGLYGLUGLUchain A and (resseq 429:442 or resseq 444:461 or resseq...AA466 - 48751 - 72
141PHEPHETHRTHRchain A and (resseq 429:442 or resseq 444:461 or resseq...AA493 - 50078 - 85
151PHEPHEASNASNchain A and (resseq 429:442 or resseq 444:461 or resseq...AA502 - 51587 - 100
161GLYGLYTHRTHRchain A and (resseq 429:442 or resseq 444:461 or resseq...AA517 - 528102 - 113
211GLNGLNGLNGLNchain B and (resseq 429:442 or resseq 444:461 or resseq...BB429 - 44214 - 27
221LEULEUGLNGLNchain B and (resseq 429:442 or resseq 444:461 or resseq...BB444 - 46129 - 46
231GLYGLYGLUGLUchain B and (resseq 429:442 or resseq 444:461 or resseq...BB466 - 48751 - 72
241PHEPHETHRTHRchain B and (resseq 429:442 or resseq 444:461 or resseq...BB493 - 50078 - 85
251PHEPHEASNASNchain B and (resseq 429:442 or resseq 444:461 or resseq...BB502 - 51587 - 100
261GLYGLYTHRTHRchain B and (resseq 429:442 or resseq 444:461 or resseq...BB517 - 528102 - 113
112LEULEUGLNGLNchain C and (resseq 430:461 or resseq 466:487 or resseq 500:527 )CC430 - 46115 - 46
122GLYGLYGLUGLUchain C and (resseq 430:461 or resseq 466:487 or resseq 500:527 )CC466 - 48751 - 72
132THRTHRCYSCYSchain C and (resseq 430:461 or resseq 466:487 or resseq 500:527 )CC500 - 52785 - 112
212LEULEUGLNGLNchain D and (resseq 430:461 or resseq 466:487 or resseq 500:527 )DD430 - 46115 - 46
222GLYGLYGLUGLUchain D and (resseq 430:461 or resseq 466:487 or resseq 500:527 )DD466 - 48751 - 72
232THRTHRCYSCYSchain D and (resseq 430:461 or resseq 466:487 or resseq 500:527 )DD500 - 52785 - 112
113TRPTRPPROPROchain L and (resseq 1:10 )LE1 - 101 - 10
213TRPTRPPROPROchain M and (resseq 1:10 )MF1 - 101 - 10

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 13449.466 Da / Num. of mol.: 4 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB7 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14451
#2: Protein/peptide cyclic peptide


Mass: 1436.500 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Sequence designed by Phase Display. Peptide was made synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 17.5% PEG3350, 0.1M Glycine, 10% Glycerol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→34 Å / Num. all: 17111 / Num. obs: 15617 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.41-2.62192
2.62-2.88193
2.88-3.25194
3.25-3.82193.1
3.82-5.4193
5.4-34191

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7_650refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.413→32.882 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7404 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 31.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 780 5 %random
Rwork0.2376 14815 --
obs0.2396 15595 92.8 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.965 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso max: 150.25 Å2 / Biso mean: 33.2281 Å2 / Biso min: 5.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.0896 Å20 Å2-2.1187 Å2
2---0.7323 Å2-0 Å2
3---0.8219 Å2
Refinement stepCycle: LAST / Resolution: 2.413→32.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 0 103 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013601
X-RAY DIFFRACTIONf_angle_d1.2054708
X-RAY DIFFRACTIONf_chiral_restr0.092512
X-RAY DIFFRACTIONf_plane_restr0.004601
X-RAY DIFFRACTIONf_dihedral_angle_d16.761276
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A705X-RAY DIFFRACTIONPOSITIONAL0.119
12B705X-RAY DIFFRACTIONPOSITIONAL0.119
21C634X-RAY DIFFRACTIONPOSITIONAL0.029
22D634X-RAY DIFFRACTIONPOSITIONAL0.029
31L91X-RAY DIFFRACTIONPOSITIONAL0.005
32M91X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4135-2.56460.32821230.30432367249089
2.5646-2.76260.37481460.30562463260993
2.7626-3.04040.33721240.26922502262694
3.0404-3.47990.26231220.21862484260694
3.4799-4.38270.23531340.20342533266795
4.3827-32.88550.2481310.22132466259791
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)
10.09860.07430.00440.1127-0.07120.1031-0.0012-0.00720.0023-0.0252-0.04250.01380.0510.0372-0.02430.12540.11640.06380.11750.00820.097713.3572-10.919317.6851
20.25450.00030.17520.19730.01020.1652-0.0482-0.06630.03480.0224-0.0189-0.00730.02780.0722-0.00410.08860.04130.02270.18040.0460.1194-6.2484-11.1744-6.0155
30.0647-0.0315-0.01860.03910.03880.0796-0.011-0.0459-0.01710.03340.02350.0224-0.0021-0.03640.04620.070.1258-0.00070.06710.0573-0.006822.1921-1.1643-9.178
40.13760.0930.03030.19240.01470.16110.00260.0260.0569-0.0879-0.0132-0.0626-0.07990.0974-0.02130.21450.03750.06120.29970.07680.1739-14.7345-0.893821.3334
50.0874-0.00370.00560.08790.01680.1225-0.0007-0.0090.00270.0006-0.01510.01340.0009-0.0176-0.00020.13710.04940.01210.1701-0.06230.0986-0.6648-11.4414.2238
60.1714-0.05550.10030.1379-0.09190.16420.00940.008-0.0078-0.00470.00030.00120.0050.01560.00310.18010.0797-0.040.21810.0170.11798.0971-11.4017-2.5158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 424:528)A0
2X-RAY DIFFRACTION2chain 'B' and (resseq 423:529)B0
3X-RAY DIFFRACTION3chain 'C' and (resseq 430:527)C0
4X-RAY DIFFRACTION4chain 'D' and (resseq 429:527)D0
5X-RAY DIFFRACTION5chain 'L'L0
6X-RAY DIFFRACTION6chain 'M'M0

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