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- PDB-7p71: The PDZ domain of MAGI1_2 complexed with the PDZ-binding motif of... -

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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


: / : / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion ...: / : / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / 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 / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / osteoclast development / calcium-dependent phospholipid binding / negative regulation of receptor internalization / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / vesicle membrane / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / alpha-actinin binding / positive regulation of exocytosis / regulation of neurogenesis / basement membrane / Smooth Muscle Contraction / bicellular tight junction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / response to activity / cell projection / cell periphery / PDZ domain binding / adherens junction / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / cell-cell junction / melanosome / cell junction / late endosome membrane / midbody / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / protein-containing complex assembly / protease binding / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / vesicle / 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 / DNA-templated transcription / calcium ion binding / host cell nucleus / Neutrophil degranulation / regulation of DNA-templated transcription / nucleolus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Unstructured region on MAGI / Unstructured region on MAGI / Annexin A2 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin ...Unstructured region on MAGI / Unstructured region on MAGI / Annexin A2 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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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

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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

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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

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