[English] 日本語
Yorodumi
- PDB-5d0j: Grb7 SH2 with inhibitor peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d0j
TitleGrb7 SH2 with inhibitor peptide
Components
  • G7-TEdFP peptide
  • Growth factor receptor-bound protein 7
KeywordsSIGNALING PROTEIN / inhibitor / SH2
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
PHOSPHATE ION / Growth factor receptor-bound protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGunzburg, M.J. / Watson, G.M. / Wilce, J.A. / Wilce, M.C.J.
CitationJournal: Sci Rep / Year: 2016
Title: Unexpected involvement of staple leads to redesign of selective bicyclic peptide inhibitor of Grb7.
Authors: Gunzburg, M.J. / Kulkarni, K. / Watson, G.M. / Ambaye, N.D. / Del Borgo, M.P. / Brandt, R. / Pero, S.C. / Perlmutter, P. / Wilce, M.C. / Wilce, J.A.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: G7-TEdFP peptide
M: G7-TEdFP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9958
Polymers56,8056
Non-polymers1902
Water19811
1
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
L: G7-TEdFP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4974
Polymers28,4023
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
M: G7-TEdFP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4974
Polymers28,4023
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.980, 94.040, 131.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid C
41chain D and segid D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid CC0
411chain D and segid DD0

-
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
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 G7-TEdFP peptide


Mass: 1021.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: sodium fluoride, PEG 3350

-
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: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.6→38.245 Å / Num. obs: 13653 / % possible obs: 99.76 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.1791 / Net I/σ(I): 9.56
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 2.83 / % possible all: 99.55

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMS

2qms


Resolution: 2.6→38.245 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 685 5.07 %
Rwork0.1869 12837 -
obs0.1899 13522 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.14 Å2 / Biso mean: 41.2794 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 2.6→38.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 10 11 3241
Biso mean--45.6 36.25 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073297
X-RAY DIFFRACTIONf_angle_d1.0774478
X-RAY DIFFRACTIONf_chiral_restr0.045521
X-RAY DIFFRACTIONf_plane_restr0.005569
X-RAY DIFFRACTIONf_dihedral_angle_d12.851097
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1786X-RAY DIFFRACTION9.281TORSIONAL
12B1786X-RAY DIFFRACTION9.281TORSIONAL
13C1786X-RAY DIFFRACTION9.281TORSIONAL
14D1786X-RAY DIFFRACTION9.281TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.80070.35391270.25082523265099
2.8007-3.08250.29021600.23532514267499
3.0825-3.52820.28811300.18042526265699
3.5282-4.44410.20531340.1572577271199
4.4441-38.24950.20621340.18092697283198
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)
10.0365-0.02910.06820.0133-0.05620.03320.31740.41070.0407-0.31750.0471-0.21690.0278-0.2691-0.00120.4321-0.0099-0.05510.4875-0.150.4416-8.93949.05138.1628
20.03450.0301-0.0010.0218-0.05010.05560.010.16950.1123-0.5329-0.00280.06130.00020.1404-0.00010.48230.0245-0.09550.648-0.0770.3348-7.104320.2936-0.1468
30.63870.0691-0.54480.0446-0.05130.4228-0.42120.1535-0.1951-0.29150.1255-0.15360.0586-0.1232-0.09410.3346-0.0332-0.02270.36580.01580.2025-2.068316.67938.0607
40.05930.05340.12870.13120.08370.12720.1570.21-0.21440.0449-0.288-0.29230.4008-0.23160.12380.24170.03130.07130.35210.02130.20580.882316.708413.6888
50.00680.02560.00780.0226-0.0187-0.01270.3761-0.1449-0.54830.1333-0.07460.04010.36570.1834-0.00020.3631-0.0831-0.09760.42670.09230.3431-0.68999.128124.6186
60.0247-0.03960.01180.0255-0.0750.07120.3756-0.23650.04450.0422-0.5806-0.1603-0.0415-0.15620.00060.3546-0.0476-0.07450.3510.0230.2912-1.264317.429923.2743
70.02380.0131-0.0628-0.0038-0.01190.05720.0805-0.30720.0927-0.11680.02360.2638-0.4885-0.4301-0.00010.3414-0.0455-0.03620.3372-0.0350.2299-9.316921.998317.0444
8-0.01310.01730.00620.00420.03360.0031-0.2437-0.6179-0.06-0.11970.11820.0068-0.2503-0.30520.00120.3848-0.0381-0.15870.61310.04230.5075-14.795715.94652.7524
90.1781-0.05370.39860.0175-0.09170.81570.03730.32970.17940.05910.12270.31840.0046-0.23410.00050.5404-0.0921-0.15460.4384-0.16110.6519-26.138714.623630.2622
100.51660.16070.11620.09050.01130.1570.2539-0.4456-0.2072-0.0333-0.13230.51310.4515-0.40510.01120.3793-0.0571-0.11250.29340.0640.4109-20.748214.999744.4697
110.182-0.1431-0.0336-0.0044-0.13730.25140.42280.3446-0.35750.0105-0.1270.35730.5056-0.10730.00990.2448-0.0526-0.0540.13310.12280.2809-17.755318.496542.584
120.8889-0.15390.07860.41260.25990.47740.599-0.03380.21960.1832-0.3329-0.1243-0.77660.00920.16360.0403-0.2236-0.20010.05040.02210.1951-14.290322.910341.2971
130.0353-0.01080.01230.0049-0.0056-0.00490.06190.37180.2748-0.292-0.02380.3919-0.0856-0.11460.00040.35020.0758-0.12460.2668-0.04170.4209-22.035126.174623.5308
140.113-0.25450.09870.519-0.20270.0960.10020.0326-0.0467-0.18160.23290.67180.1210.41990.02410.3526-0.02020.01530.232-0.03660.2211-14.362726.590227.3607
150.0686-0.13720.04470.0384-0.1350.4707-0.07860.13020.06040.1768-0.1081-0.11760.48790.83720.00280.32830.0334-0.02080.34530.05690.2793-10.726716.123334.8058
160.0637-0.2924-0.0680.9050.14611.1383-0.04640.11-0.06031.14540.56480.5142-0.09340.42250.20520.2317-0.1523-0.01110.0235-0.12470.2108-24.0757-5.649732.9305
170.6408-0.59390.33470.3714-0.0081.20040.03110.38-0.16070.0917-0.22030.039-0.11660.0673-0.60350.1141-0.04650.07040.1496-0.08040.1717-20.179-9.245422.3517
180.0304-0.0593-0.01980.0773-0.04820.03610.2772-0.03980.4114-0.3333-0.0520.15180.1502-0.08960.00010.3124-0.07550.04760.2416-0.12390.376-17.47582.0871-3.6004
190.89390.2028-0.45741.208-0.06531.6981-0.0766-0.3025-0.1356-0.28820.00980.34780.06730.3385-0.3570.1687-0.10570.02430.2454-0.10060.1773-14.1393-8.7751-6.9568
200.4844-0.24770.39670.2882-0.26680.4222-0.12370.22460.08050.4158-0.22070.13250.3889-0.1765-0.12660.2619-0.08270.10160.3072-0.12220.2639-25.4119-9.60812.9792
210.14590.0134-0.35010.0187-0.00290.5257-0.0659-0.3690.06290.08360.03130.19820.08810.83080.00250.2564-0.13220.0560.364-0.04840.1966-13.4255-9.00975.0641
220.04-0.0027-0.02160.06580.12160.2307-0.15920.0503-0.03410.287-0.02570.09790.15180.18040.00360.4946-0.25360.00890.58920.08180.3696.466321.155410.8983
230.00850.00890.01150.02560.00050.0134-0.28290.1304-0.1342-0.2214-0.0094-0.2282-0.0974-0.0992-0.00050.4895-0.0690.00740.3625-0.09090.3864-23.8649-17.0634-5.2801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 426 through 437 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 438 through 454 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 455 through 475 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 476 through 487 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 488 through 494 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 495 through 504 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 505 through 523 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 524 through 531 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 422 through 427 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 428 through 447 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 448 through 466 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 467 through 485 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 486 through 494 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 495 through 504 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 505 through 529 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 429 through 475 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 476 through 530 )C0
18X-RAY DIFFRACTION18chain 'D' and (resid 424 through 437 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 438 through 475 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 476 through 504 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 505 through 528 )D0
22X-RAY DIFFRACTION22chain 'L' and (resid 3 through 9 )L0
23X-RAY DIFFRACTION23chain 'M' and (resid 1 through 8 )M0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more