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- PDB-2qms: Crystal structure of a signaling molecule -

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Basic information

Entry
Database: PDB / ID: 2qms
TitleCrystal structure of a signaling molecule
ComponentsGrowth factor receptor-bound protein 7
KeywordsSIGNALING PROTEIN / SH2 domain / alpha/beta fold
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsPorter, C.J. / Wilce, M.C. / Wilce, J.A.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation.
Authors: Porter, C.J. / Matthews, J.M. / Mackay, J.P. / Pursglove, S.E. / Schmidberger, J.W. / Leedman, P.J. / Pero, S.C. / Krag, D.N. / Wilce, M.C. / Wilce, J.A.
History
DepositionJul 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,43511
Polymers54,7634
Non-polymers6727
Water3,261181
1
A: Growth factor receptor-bound protein 7
hetero molecules

C: Growth factor receptor-bound protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7666
Polymers27,3812
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area12080 Å2
MethodPISA
2
B: Growth factor receptor-bound protein 7
hetero molecules

D: Growth factor receptor-bound protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6705
Polymers27,3812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area2260 Å2
ΔGint-10 kcal/mol
Surface area12180 Å2
MethodPISA
3
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7666
Polymers27,3812
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6705
Polymers27,3812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.649, 63.904, 105.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

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Components

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


Mass: 13690.711 Da / Num. of mol.: 4 / Fragment: SH2 domain (residues 415-532)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB7 / Plasmid: pGex4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3).pLysS / References: UniProt: Q14451
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1M sodium citrate pH6.1, 22.5% PEG 4000, 0.2M Ammonium sulphate, 5 % glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→44.7 Å / Num. obs: 25401 / % possible obs: 99.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1269 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.502 / Cor.coef. Fo:Fc: 0.544
Highest resolutionLowest resolution
Rotation4 Å44.74 Å
Translation4 Å44.74 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.16 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1269 5 %RANDOM
Rwork0.201 ---
obs0.203 25218 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.54 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 35 181 3949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213757
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.975086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35922.727187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35915660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8221539
X-RAY DIFFRACTIONr_chiral_restr0.0940.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022835
X-RAY DIFFRACTIONr_nbd_refined0.2020.21547
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.2159
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.229
X-RAY DIFFRACTIONr_mcbond_it1.77622356
X-RAY DIFFRACTIONr_mcangle_it2.77133626
X-RAY DIFFRACTIONr_scbond_it1.77221580
X-RAY DIFFRACTIONr_scangle_it2.6131455
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 89 -
Rwork0.254 1731 -
all-1820 -
obs--99.34 %

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