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- PDB-7mp3: Grb7-SH2 domain in complex with bicyclic peptide B8 -

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Basic information

Entry
Database: PDB / ID: 7mp3
TitleGrb7-SH2 domain in complex with bicyclic peptide B8
Components
  • Growth factor receptor-bound protein 7
  • bicyclic peptide B8
KeywordsSIGNALING PROTEIN / Grb7 / SH2 / bicyclic-peptide / inhibitor
Function / homology
Function and homology information


GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / stress granule assembly / Tie2 Signaling / Downstream signal transduction / phosphatidylinositol binding / 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 / Downstream signal transduction / phosphatidylinositol binding / 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 / 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 / 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
Similarity search - Domain/homology
Growth factor receptor-bound protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsColson, R. / Wilce, M.C.J. / Wilce, J.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomedicines / Year: 2022
Title: Enhancing the Bioactivity of Bicyclic Peptides Targeted to Grb7-SH2 by Restoring Cell Permeability.
Authors: Sturre, N.P. / Colson, R.N. / Shah, N. / Watson, G.M. / Yang, X. / Wilce, M.C.J. / Price, J.T. / Wilce, J.A.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Apr 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.entity_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: bicyclic peptide B8
N: bicyclic peptide B8


Theoretical massNumber of molelcules
Total (without water)57,5766
Polymers57,5766
Non-polymers00
Water93752
1
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
L: bicyclic peptide B8


Theoretical massNumber of molelcules
Total (without water)28,7883
Polymers28,7883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
N: bicyclic peptide B8


Theoretical massNumber of molelcules
Total (without water)28,7883
Polymers28,7883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.156, 53.122, 54.809
Angle α, β, γ (deg.)103.983, 101.997, 100.048
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 425 and (name N or name...
d_2ens_1(chain "C" and (resid 425 through 429 or (resid 430...
d_1ens_2(chain "B" and ((resid 429 through 430 and (name N...
d_2ens_2(chain "D" and (resid 429 through 460 or resid 464 through 527))
d_1ens_3chain "L"
d_2ens_3chain "N"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILETHRA1 - 102
d_21ens_1ILETHRC1 - 102
d_11ens_2GLNCYSB1 - 96
d_21ens_2GLNSERD2 - 33
d_22ens_2PROCYSD36 - 99
d_11ens_3LYSPROE1 - 10
d_12ens_3KCUKCUF
d_21ens_3LYSPROG1 - 10
d_22ens_3KCUKCUH

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.964493129116, 0.262238043966, 0.0313721562145), (0.263707986759, 0.949679507889, 0.169017543512), (0.0145293361314, 0.171289347573, -0.985113626847)-5.24390176116, 3.30623998564, -28.8041660811
2given(0.803346765472, 0.314163389446, 0.505900522967), (0.313868415735, -0.945320404459, 0.0886338000812), (0.50608358204, 0.0875825190562, -0.858026054584)-9.37062873604, 17.5200842589, 22.195026286
3given(-0.678190072262, 0.60601793194, -0.415692785662), (-0.56438949549, -0.791789172078, -0.233526025019), (-0.470662005335, 0.0762376097955, 0.879013710693)-26.8404562901, 10.2821261596, 44.7272612842
4given(0.800442172442, 0.325040252155, 0.503628000667), (0.32303740611, -0.941673016565, 0.0943332609824), (0.504915005551, 0.0871823626256, -0.858754955046)-9.39270321818, 17.586809633, 22.2074125642

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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.: 4 / Fragment: SH2 domain
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: Protein/peptide bicyclic peptide B8


Mass: 1406.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M NaCl, 0.1M BIS TRIS pH 6.6, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.55→52.5 Å / Num. obs: 14036 / % possible obs: 98.18 % / Redundancy: 4.2 % / Biso Wilson estimate: 35.42 Å2 / CC1/2: 0.912 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.086 / Net I/σ(I): 4.94
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 1408 / CC1/2: 0.564 / Rpim(I) all: 0.4345 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS2021data reduction
Aimless0.7.4data scaling
MOLREP13.07.2020phasing
Coot0.9.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEQ

5eeq


Resolution: 2.55→51.33 Å / SU ML: 0.3821 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.4663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2642 653 4.65 %
Rwork0.2209 13383 -
obs0.223 14036 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.56 Å2
Refinement stepCycle: LAST / Resolution: 2.55→51.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 20 52 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193281
X-RAY DIFFRACTIONf_angle_d0.49674433
X-RAY DIFFRACTIONf_chiral_restr0.0377497
X-RAY DIFFRACTIONf_plane_restr0.0039569
X-RAY DIFFRACTIONf_dihedral_angle_d15.5677449
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.601604371758
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.553929563497
ens_3d_2LX-RAY DIFFRACTIONTorsion NCS0.889913401756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.750.31651400.26512645X-RAY DIFFRACTION97.48
2.75-3.020.36321110.26972694X-RAY DIFFRACTION97.8
3.02-3.460.30821280.23022680X-RAY DIFFRACTION98.28
3.46-4.360.22731500.19482653X-RAY DIFFRACTION98.52
4.36-51.330.23561240.20592711X-RAY DIFFRACTION98.92
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)
14.87689819396-0.7259038963580.3847309925974.851212950670.09217589082784.714330871210.1221072084840.110304770513-0.15256067529-0.12835844553-0.1538504787650.1537036089760.1578108850620.1311535082840.02655827385580.3350853525670.02322432265060.0248291926360.1701790561970.0004424663001630.198796793751-0.740657479921-0.254772832149-0.707203890097
24.74102436711-1.026096821831.288050510213.603941400210.2399209777185.699142106660.1080033386830.296196187357-0.0989752499411-0.177453538189-0.04376494972790.189985630674-0.203310382054-0.0450096596936-0.0606111076060.2634594749640.00766572076043-0.006460402523770.164835585225-0.008229611002190.218880490146-4.953060804513.22696328191-27.8895385793
33.744742407730.0660937995682-0.5398007192465.147296130020.3500447551914.580966520440.1374111748710.006949666615680.1112634149820.110682150333-0.0848454972088-0.0773143212236-0.2380744392440.0850118876829-0.02388578937150.2965616336130.0490761432943-0.003185217875210.1919749882010.008828745444210.204261647259-10.568286016717.403408162722.4425974194
43.46699943558-0.837408673358-0.3041297765733.910475300880.02488971540486.116613059060.181338404497-0.15465051709-0.03167940659720.0465128106525-0.1339136563630.01699594072330.0823368411911-0.200046878639-0.0192158299980.2651854917480.01605311683830.005973408264610.1774880581340.01262348754010.245261760292-25.809785230710.888534361744.2596580054
58.40067048346-4.171417130034.449370225586.49945738428-3.289445468872.6648902254-0.183121078016-0.1640880492750.9085476389080.0801909758971-0.0972585437439-0.4175221732710.00670358842974-0.2618468845680.2954004864040.5557498990680.01922051431580.1028268250240.2543354194110.03440186674260.284790144557-3.6744097097612.31867572193.1956679856
60.1770165878110.260277319477-0.9671917080190.385437392409-1.460985065068.11100746236-0.362764588549-0.0803879248775-0.0450592954632-0.4370055329350.193342699319-0.2532950354110.337713696084-0.4697146203960.162636841770.332577791472-0.00886129975066-0.06627646131440.2558473293-0.01418344548740.303521794351-6.750770185755.0972278944618.6948730226
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 425 through 528)AA425 - 5281 - 102
22(chain 'B' and resid 429 through 528)BB429 - 5281 - 97
33(chain 'C' and resid 425 through 528)CC425 - 5281 - 102
44(chain 'D' and resid 428 through 527)DD428 - 5271 - 99
55(chain 'L' and resid 1 through 10)LE1 - 101 - 10
66(chain 'N' and resid 1 through 10)NG1 - 101 - 10

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