[English] 日本語
Yorodumi
- PDB-3pqz: Grb7 SH2 with peptide -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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
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

-
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: 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-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 429:442 or resseq 444:461 or resseq...A429 - 442
121chain A and (resseq 429:442 or resseq 444:461 or resseq...A444 - 461
131chain A and (resseq 429:442 or resseq 444:461 or resseq...A466 - 487
141chain A and (resseq 429:442 or resseq 444:461 or resseq...A493 - 500
151chain A and (resseq 429:442 or resseq 444:461 or resseq...A502 - 515
161chain A and (resseq 429:442 or resseq 444:461 or resseq...A517 - 528
211chain B and (resseq 429:442 or resseq 444:461 or resseq...B429 - 442
221chain B and (resseq 429:442 or resseq 444:461 or resseq...B444 - 461
231chain B and (resseq 429:442 or resseq 444:461 or resseq...B466 - 487
241chain B and (resseq 429:442 or resseq 444:461 or resseq...B493 - 500
251chain B and (resseq 429:442 or resseq 444:461 or resseq...B502 - 515
261chain B and (resseq 429:442 or resseq 444:461 or resseq...B517 - 528
112chain C and (resseq 430:461 or resseq 466:487 or resseq 500:527 )C430 - 461
122chain C and (resseq 430:461 or resseq 466:487 or resseq 500:527 )C466 - 487
132chain C and (resseq 430:461 or resseq 466:487 or resseq 500:527 )C500 - 527
212chain D and (resseq 430:461 or resseq 466:487 or resseq 500:527 )D430 - 461
222chain D and (resseq 430:461 or resseq 466:487 or resseq 500:527 )D466 - 487
232chain D and (resseq 430:461 or resseq 466:487 or resseq 500:527 )D500 - 527
113chain L and (resseq 1:10 )L1 - 10
213chain M and (resseq 1:10 )M1 - 10

NCS ensembles :
ID
1
2
3

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://pdbjlvh1.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