[English] 日本語
Yorodumi
- PDB-7p71: The PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p71
TitleThe PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of HPV35-E6
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
  • Protein E6
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex
Function / homology
Function and homology information


AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / symbiont-mediated perturbation of host apoptosis / positive regulation of vesicle fusion / myelin sheath adaxonal region / negative regulation of low-density lipoprotein particle receptor catabolic process ...AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / symbiont-mediated perturbation of host apoptosis / positive regulation of vesicle fusion / myelin sheath adaxonal region / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / positive regulation of cell-cell adhesion / cadherin binding involved in cell-cell adhesion / cornified envelope / endothelial cell morphogenesis / Schmidt-Lanterman incisure / vesicle budding from membrane / plasma membrane protein complex / calcium-dependent phospholipid binding / osteoclast development / negative regulation of receptor internalization / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / alpha-actinin binding / basement membrane / positive regulation of exocytosis / Smooth Muscle Contraction / regulation of neurogenesis / bicellular tight junction / cytoskeletal protein binding / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / lipid droplet / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lung development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / response to activity / cell periphery / cell projection / adherens junction / PDZ domain binding / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / azurophil granule lumen / cell-cell junction / late endosome membrane / cell junction / melanosome / : / protein-containing complex assembly / protease binding / midbody / angiogenesis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / basolateral plasma membrane / vesicle / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / early endosome / cell surface receptor signaling pathway / cell adhesion / endosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / lysosomal membrane / calcium ion binding / DNA-templated transcription / Neutrophil degranulation / regulation of DNA-templated transcription / nucleolus / host cell nucleus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Unstructured region on MAGI / Unstructured region on MAGI / Annexin A2 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin ...Unstructured region on MAGI / Unstructured region on MAGI / Annexin A2 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Annexin A2 / Protein E6 / Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus 35
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGogl, G. / Cousido-Siah, A. / Trave, G.
CitationJournal: Nat Commun / Year: 2022
Title: Quantitative fragmentomics allow affinity mapping of interactomes.
Authors: Gogl, G. / Zambo, B. / Kostmann, C. / Cousido-Siah, A. / Morlet, B. / Durbesson, F. / Negroni, L. / Eberling, P. / Jane, P. / Nomine, Y. / Zeke, A. / Ostergaard, S. / Monsellier, E. / Vincentelli, R. / Trave, G.
History
DepositionJul 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 5, 2023Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
C: Protein E6
D: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,24618
Polymers99,2734
Non-polymers97314
Water27015
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
C: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,26510
Polymers49,6362
Non-polymers6298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-45 kcal/mol
Surface area21080 Å2
MethodPISA
2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
D: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9818
Polymers49,6362
Non-polymers3456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-40 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.130, 61.030, 98.990
Angle α, β, γ (deg.)90.000, 97.330, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2 / Atrophin-1-interacting protein 3 / AIP-3 / BAI1-associated protein 1 / BAP-1 / Membrane-associated ...Atrophin-1-interacting protein 3 / AIP-3 / BAI1-associated protein 1 / BAP-1 / Membrane-associated guanylate kinase inverted 1 / MAGI-1 / Trinucleotide repeat-containing gene 19 protein / WW domain-containing protein 3 / WWP3 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 48099.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: MAGI1, AIP3, BAIAP1, BAP1, TNRC19, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D
Production host: Escherichia coli (E. coli) / References: UniProt: Q96QZ7, UniProt: P07355
#2: Protein/peptide Protein E6


Mass: 1536.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: N-terminal biotin-ttds label / Source: (synth.) Human papillomavirus 35 / References: UniProt: P27228

-
Non-polymers , 4 types, 29 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-25% polyethylene glycol 3000, 100 mM sodium citrate buffered at pH 5.5 and 100 mM trisodium-citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48 Å / Num. obs: 33417 / % possible obs: 94.4 % / Redundancy: 4.5 % / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 19.06
Reflection shellResolution: 2.6→2.67 Å / Mean I/σ(I) obs: 1.69 / Num. unique obs: 2471 / CC1/2: 0.852 / Rrim(I) all: 1.11 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7D

5n7d


Resolution: 2.6→47.64 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 1641 4.95 %
Rwork0.2413 31481 -
obs0.2433 33122 93.59 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 254.8 Å2 / Biso mean: 103.2257 Å2 / Biso min: 47.29 Å2
Refinement stepCycle: final / Resolution: 2.6→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6635 0 51 15 6701
Biso mean--113.68 68.24 -
Num. residues----854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.67650.60341260.5281243588
2.6765-2.76290.42551570.4318261094
2.7629-2.86160.37261380.3302273499
2.8616-2.97620.34161460.3111273298
2.9762-3.11160.34831380.2965275299
3.1116-3.27560.37881380.3142274499
3.2756-3.48080.30541210.3145234584
3.4808-3.74950.43751390.3606236485
3.7495-4.12660.24961060.2546228581
4.1266-4.72330.27261330.1875280199
4.7233-5.9490.21871550.1954279699
5.949-47.640.1641440.1572288399
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)
11.4852.665-0.20374.673-0.24130.06760.2037-0.02350.0512-0.31770.24070.7708-0.03450.0321-0.41630.7859-0.1558-0.24360.88350.08541.2556336.8127-36.7364434.7081
23.3465-1.0064-0.50562.65730.32121.26640.01930.28970.0044-0.38170.0380.25310.1067-0.1163-0.05470.8946-0.0837-0.01350.43070.04880.4855366.0448-22.2207430.8983
30.0943-0.5568-0.15345.93580.86010.1712-0.1958-0.03460.6955-0.3716-0.23520.1951-0.57230.01290.45581.88880.0774-0.57921.67680.2062.0084355.4724-19.4162375.8101
43.72581.53222.02342.90871.60562.44040.196-0.24170.09210.3154-0.39870.50340.1626-0.4330.18990.6866-0.02740.07280.79550.00790.5237363.2499-45.4742392.5634
55.776.78872.71099.3914.72757.1423-0.0043-2.6320.35280.0546-0.1926-0.8406-0.9069-0.21820.18560.7321-0.2159-0.17061.36410.1481.7804347.9912-50.7787428.9963
65.6457-5.87385.55586.2178-5.82435.4854-0.57951.3428-3.576-3.36191.5352.54381.9006-1.237-0.90942.3626-0.0136-0.4271.5514-0.03362.4265348.7563-21.7353383.282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 456 through 632 )A456 - 632
2X-RAY DIFFRACTION2chain 'A' and (resid 633 through 878 )A633 - 878
3X-RAY DIFFRACTION3chain 'B' and (resid 459 through 573 )B459 - 573
4X-RAY DIFFRACTION4chain 'B' and (resid 574 through 878 )B574 - 878
5X-RAY DIFFRACTION5chain 'C' and (resid 143 through 149 )C143 - 149
6X-RAY DIFFRACTION6chain 'D' and (resid 146 through 149 )D146 - 149

+
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