[English] 日本語
Yorodumi
- PDB-7bqg: Complex structure of SAV1 and Dendrin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bqg
TitleComplex structure of SAV1 and Dendrin
ComponentsProtein salvador homolog 1,Dendrin
KeywordsSIGNALING PROTEIN / Hippo pathway / WW domain / SAV1 / Dendrin
Function / homology
Function and homology information


Signaling by Hippo / intestinal epithelial cell differentiation / regulation of stem cell population maintenance / positive regulation of hippo signaling / negative regulation of cardiac muscle cell proliferation / lung epithelial cell differentiation / hippo signaling / regulation of organ growth / transcription regulator activator activity / dendritic spine membrane ...Signaling by Hippo / intestinal epithelial cell differentiation / regulation of stem cell population maintenance / positive regulation of hippo signaling / negative regulation of cardiac muscle cell proliferation / lung epithelial cell differentiation / hippo signaling / regulation of organ growth / transcription regulator activator activity / dendritic spine membrane / ventricular septum morphogenesis / hair follicle development / negative regulation of hippo signaling / positive regulation of fat cell differentiation / keratinocyte differentiation / protein serine/threonine kinase activator activity / negative regulation of epithelial cell proliferation / presynapse / molecular adaptor activity / perikaryon / DNA-binding transcription factor activity, RNA polymerase II-specific / postsynaptic membrane / protein stabilization / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / apoptotic process / dendrite / endoplasmic reticulum membrane / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Dendrin / Scaffold protein salvador / Nephrin and CD2AP-binding protein, Dendrin / SARAH domain / SARAH domain profile. / WW domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
: / Dendrin / Protein salvador homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55010861961 Å
AuthorsLin, Z. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Cell Rep / Year: 2020
Title: A WW Tandem-Mediated Dimerization Mode of SAV1 Essential for Hippo Signaling.
Authors: Lin, Z. / Xie, R. / Guan, K. / Zhang, M.
History
DepositionMar 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: Protein salvador homolog 1,Dendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4384
Polymers10,3201
Non-polymers1173
Water1,65792
1
A: Protein salvador homolog 1,Dendrin
hetero molecules

A: Protein salvador homolog 1,Dendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8758
Polymers20,6412
Non-polymers2356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area4230 Å2
ΔGint-26 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.803, 43.084, 99.385
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-301-

K

21A-303-

K

-
Components

#1: Protein Protein salvador homolog 1,Dendrin / 45 kDa WW domain protein / mWW45


Mass: 10320.290 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sav1, Ww45, Wwp3, Ddn, Gm748, Kiaa0749 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VEB2, UniProt: Q80TS7
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2% w/v PEG 2000 MME and 100 mM BIS-TRIS propane (pH 9.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 11875 / % possible obs: 99.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 12.8744218645 Å2 / CC1/2: 0.99 / Net I/σ(I): 39.1
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 599 / CC1/2: 0.69

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BQF

7bqf


Resolution: 1.55010861961→49.6925 Å / SU ML: 0.149561517705 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.1462025962
RfactorNum. reflection% reflection
Rfree0.216578983246 1189 10.0126315789 %
Rwork0.177694973739 --
obs0.181655015371 11875 95.220912517 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.5003240728 Å2
Refinement stepCycle: LAST / Resolution: 1.55010861961→49.6925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms696 0 3 92 791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624081380489753
X-RAY DIFFRACTIONf_angle_d1.03131247291043
X-RAY DIFFRACTIONf_chiral_restr0.037720092214297
X-RAY DIFFRACTIONf_plane_restr0.00521105024004139
X-RAY DIFFRACTIONf_dihedral_angle_d12.1452183019271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5502-1.62070.2697638954351240.2261281519721096X-RAY DIFFRACTION79.2722547109
1.6207-1.70610.271494715081390.192501708671272X-RAY DIFFRACTION92.3429319372
1.7061-1.8130.2463161694041480.1761827590481318X-RAY DIFFRACTION95.5671447197
1.813-1.9530.2244942620831510.1739210871671349X-RAY DIFFRACTION97.0245795602
1.953-2.14950.2008243821431530.1611185123741370X-RAY DIFFRACTION99.3476842792
2.1495-2.46060.2079246788061540.1883167573051387X-RAY DIFFRACTION98.7820512821
2.4606-3.10.2477124739731560.2003697294591412X-RAY DIFFRACTION99.872611465
3.1-490.1871014137221640.1595662675121482X-RAY DIFFRACTION99.0969295605
Refinement TLS params.Method: refined / Origin x: 38.4734067236 Å / Origin y: 12.2274488768 Å / Origin z: 17.0675130407 Å
111213212223313233
T0.0918675070246 Å20.0108181817598 Å2-0.0053059500598 Å2-0.106702545478 Å20.00328914767923 Å2--0.120246215607 Å2
L0.0921946759338 °2-0.0694245414299 °2-0.337143663745 °2-0.206491020959 °20.157191144039 °2--1.22545382743 °2
S0.0316861378955 Å °-0.0101535419496 Å °-0.0383063312652 Å °-0.00596067531414 Å °-0.0116562721868 Å °0.00915819934473 Å °-0.0468093238617 Å °-0.0844047060775 Å °-0.024930326036 Å °
Refinement TLS groupSelection details: all

+
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