[English] 日本語
Yorodumi
- PDB-6ywz: Crystal structure of SHANK1 PDZ in complex with a peptide-small m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ywz
TitleCrystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid
ComponentsSH3 and multiple ankyrin repeat domains protein 1
KeywordsPEPTIDE BINDING PROTEIN / protein-protein interactions PDZ domain / hybrid structures / fragment-based drug discovery / beta-sheets / acylhydrazone
Function / homology
Function and homology information


somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior ...somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / Neurexins and neuroligins / adult behavior / positive regulation of dendritic spine development / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / excitatory synapse / long-term memory / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / SH3 domain binding / scaffold protein binding / postsynaptic membrane / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / dendrite / protein-containing complex binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
ARGININE / LEUCINE / DI(HYDROXYETHYL)ETHER / Chem-PWN / THREONINE / SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsHegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Lian, L.J. / Trinh, C.H. / Sessions, R.B. / Edwards, T.A. / Wilson, A.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/N035267/1 United Kingdom
European CommissionMSCA-IF-2016-749012 United Kingdom
Royal SocietySRF/R1/191087 United Kingdom
CitationJournal: Chem Sci / Year: 2021
Title: Identification of beta-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation.
Authors: Hegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Lian, L.Y. / Trinh, C.H. / Sessions, R.B. / Edwards, T.A. / Wilson, A.J.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: SH3 and multiple ankyrin repeat domains protein 1
A: SH3 and multiple ankyrin repeat domains protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,13611
Polymers24,6832
Non-polymers1,4549
Water1,36976
1
B: SH3 and multiple ankyrin repeat domains protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1216
Polymers12,3411
Non-polymers7805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SH3 and multiple ankyrin repeat domains protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0155
Polymers12,3411
Non-polymers6744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.566, 65.973, 86.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein SH3 and multiple ankyrin repeat domains protein 1 / Shank1 / Somatostatin receptor-interacting protein / SSTRIP


Mass: 12341.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHANK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y566

-
Non-polymers , 6 types, 85 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Chemical ChemComp-PWN / 2-[(~{E})-(4-oxidanylidenebutanoylhydrazinylidene)methyl]benzoic acid


Mass: 248.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O4
#4: Chemical ChemComp-THR / THREONINE / Threonine


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#5: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#6: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7 PEG 400 35%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.12→65.97 Å / Num. obs: 15149 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 45.69 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.044 / Rrim(I) all: 0.116 / Net I/σ(I): 7.4
Reflection shellResolution: 2.12→2.16 Å / Rmerge(I) obs: 1.234 / Num. unique obs: 4553 / CC1/2: 0.64 / Rpim(I) all: 0.584

-
Processing

Software
NameVersionClassification
REFMAC5.5.0026refinement
PHENIX1.17.1_3660refinement
DIALSdata processing
Aimlessdata scaling
pointlessdata scaling
PHASERphasing
Cootmodel building
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q3O

1q3o


Resolution: 2.12→43.45 Å / SU ML: 0.2345 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.5013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 709 4.71 %
Rwork0.2145 14356 -
obs0.216 15065 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.81 Å2
Refinement stepCycle: LAST / Resolution: 2.12→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 97 76 1783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081746
X-RAY DIFFRACTIONf_angle_d0.89492351
X-RAY DIFFRACTIONf_chiral_restr0.0565263
X-RAY DIFFRACTIONf_plane_restr0.0058305
X-RAY DIFFRACTIONf_dihedral_angle_d13.6961292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.280.36291360.32682800X-RAY DIFFRACTION99.63
2.28-2.510.31831660.27772800X-RAY DIFFRACTION99.7
2.51-2.880.23351310.25062858X-RAY DIFFRACTION99.87
2.88-3.620.26991290.22022885X-RAY DIFFRACTION99.7
3.63-43.450.21021470.17973013X-RAY DIFFRACTION99.81
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)
11.104379447030.140383751997-0.944096078710.5733321749470.8107945415062.141742053290.2800063130230.1101262506250.457317482178-0.00581575499723-0.0454817643454-0.0971793823696-0.5961105821290.127024648025-0.223067658510.4624474589040.04486981084940.05961557552740.4281002502810.08264040062390.4249632151989.112965463646.253644089631.8008973521
20.1337032079550.230519214744-0.4432512774163.20527613786-2.308802920495.57721646762-0.117679786266-0.2824350125760.104179130890.109177340776-0.225139839660.1971504832970.6070738283140.8072699284130.3234447865630.5184778953770.0500315669645-0.004163197423080.4264670637780.04583664132990.57399958122111.8665509934-8.2409223101411.4980042967
35.399805701630.788128050978-3.131122045293.852629284020.984072865626.14950137757-0.01374421557060.004624672733480.007196937658650.270744556897-0.006357469458360.08084492483030.02524509390360.310795361158-0.01030818119370.329880673426-0.00228096055101-0.02148076184150.3467853318140.08217256960530.37143543758611.08551889540.3198321490413.08245611057
42.011201634781.353379840063.004209171831.300340622822.9146886166.5212706559-0.009700767011191.111114366690.943625784059-0.510851851856-0.389547930412-0.0164517333385-0.0520366475011-1.968424148610.3976182874111.168523037280.286054661680.2731831476780.7256198157230.1614281545020.601898828051-0.097113073600111.17284660022.52170306273
52.590347427890.375976702938-0.8468593682662.74771465491-0.5019872453852.895414230950.104303681415-0.188401756080.06434207812110.06089849729250.02375436122210.0699758880349-0.253500912885-0.524063711774-0.1179540937480.348065894732-0.0288909150873-0.02503840946990.476972166142-0.1001624710770.35053760435-11.97805814584.7224614877930.7006884698
62.59821607579-0.301315334929-2.051194898741.39510981490.7490628811044.963085989520.4644599552371.70223135096-0.733597290803-1.12278158232-0.585624495791-0.115361213335-0.700948660755-1.498283200580.01392439002620.6609342935010.0606864443717-0.02123670877310.635640193781-0.1795701499440.552511916453-10.1289772455-2.2385648410813.9145464541
72.644005143191.5285004134-0.802030930933.369611371620.6481259272283.984098424170.1038731795540.2975424139440.10119357112-0.3374630351460.02364040365550.030672110576-0.509979747241-0.541234885394-0.1376491236460.4354453601610.116764701212-0.06002847063980.478688416922-0.06134341844190.401157327997-14.43145546435.6344600298623.7192953323
84.074206395781.80618217465-0.1014541970972.23838259605-0.2798452822464.2939798693-0.0471212164640.277221699783-1.507865046280.136749045338-0.02664054161530.09998191540961.31876325678-0.106219890353-0.02504460214690.47437889793-0.068531397256-0.05865482707980.405124943403-0.1179520224970.693908312782-10.7524215238-8.5483116177324.9535844927
93.006113405890.733970613186-2.984132203942.23308767861-3.030275953688.080319524680.261557391019-0.02123877748420.1719760990550.1245610350540.1480535102070.168630724859-0.4276645318780.0947081806838-0.4955619104950.4312024067420.0539683686198-0.05372111149230.496552157367-0.1121261691850.45639944329-8.342702186923.6267988316124.871464282
103.228986115250.06608362446891.026052254412.40665449346-1.839107476711.90679436814-0.4317707819120.6790227997820.37723325586-0.0316619793430.0846442242293-0.0324740858416-0.2155722976170.319626716550.5207710004450.535696801709-0.050983110749-0.0547794822490.740492610592-0.2691739342560.642716675703-20.5151195008-4.0674022382121.9435787852
117.487561343710.346920972399-3.536914794628.653550577280.1205668725922.501802198040.46416281242-1.43915679669-0.007020916005870.2557256523580.868747054160.366266910529-0.6365719422430.341433589237-1.539106175240.4480017798760.01555356201640.06204219779410.7573459637570.1403634796790.76872224677821.4781917654-3.97018382362.16870991478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 651 through 675 )
2X-RAY DIFFRACTION2chain 'B' and (resid 676 through 690 )
3X-RAY DIFFRACTION3chain 'B' and (resid 691 through 759 )
4X-RAY DIFFRACTION4chain 'A' and (resid 651 through 657 )
5X-RAY DIFFRACTION5chain 'A' and (resid 658 through 675 )
6X-RAY DIFFRACTION6chain 'A' and (resid 676 through 699 )
7X-RAY DIFFRACTION7chain 'A' and (resid 700 through 725 )
8X-RAY DIFFRACTION8chain 'A' and (resid 726 through 745 )
9X-RAY DIFFRACTION9chain 'A' and (resid 746 through 758 )
10X-RAY DIFFRACTION10chain 'C'
11X-RAY DIFFRACTION11chain 'D'

+
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