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- PDB-6twu: MAGI1_2 complexed with a phosphomimetic 16E6 peptide -

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Basic information

Entry
Database: PDB / ID: 6twu
TitleMAGI1_2 complexed with a phosphomimetic 16E6 peptide
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
  • Protein E6
KeywordsPEPTIDE BINDING PROTEIN / phosphorylation / motif / PDZ domain
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / 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 ...symbiont-mediated suppression of host transcription / 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 / regulation of proteolysis / calcium-dependent phospholipid binding / negative regulation of receptor internalization / activation of GTPase activity / collagen fibril organization / S100 protein binding / Dissolution of Fibrin Clot / virion binding / osteoclast development / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / positive regulation of exocytosis / alpha-actinin binding / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / bicellular tight junction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoskeletal protein binding / lipid droplet / cell-matrix adhesion / response to activity / cell projection / PDZ domain binding / cell periphery / : / adherens junction / lung development / sarcolemma / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / calcium channel activity / 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 / symbiont-mediated perturbation of host ubiquitin-like protein modification / basolateral plasma membrane / angiogenesis / protein-containing complex assembly / collagen-containing extracellular matrix / protease binding / vesicle / host cell cytoplasm / cell surface receptor signaling pathway / early endosome / cell adhesion / endosome / lysosomal membrane / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / calcium ion binding / Neutrophil degranulation / nucleolus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Unstructured region on MAGI / Unstructured region on MAGI / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin ...Unstructured region on MAGI / Unstructured region on MAGI / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin A2 / 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 / Protein E6 / Annexin A2 / Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGogl, G. / Cousido-Siah, A. / Trave, G.
CitationJournal: Structure / Year: 2020
Title: Dual Specificity PDZ- and 14-3-3-Binding Motifs: A Structural and Interactomics Study.
Authors: Gogl, G. / Jane, P. / Caillet-Saguy, C. / Kostmann, C. / Bich, G. / Cousido-Siah, A. / Nyitray, L. / Vincentelli, R. / Wolff, N. / Nomine, Y. / Sluchanko, N.N. / Trave, G.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,75820
Polymers97,4643
Non-polymers1,29417
Water1,11762
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6779
Polymers48,1001
Non-polymers5778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-32 kcal/mol
Surface area20580 Å2
MethodPISA
2
B: 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)50,08111
Polymers49,3642
Non-polymers7179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-51 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.160, 96.440, 197.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#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: 1264.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16 / References: UniProt: P03126

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Non-polymers , 4 types, 79 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3000, 100mM Na-citrate (pH5.5), 100mM Na-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: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.3 Å / Num. obs: 46699 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 65.37 Å2 / CC1/2: 1 / Net I/σ(I): 1.22
Reflection shellResolution: 2.4→2.46 Å / Mean I/σ(I) obs: 1.22 / Num. unique obs: 3389 / CC1/2: 0.489

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Processing

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

5n7d


Resolution: 2.4→48.22 Å / SU ML: 0.3968 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4691
RfactorNum. reflection% reflection
Rfree0.255 2306 4.95 %
Rwork0.2163 --
obs0.2182 46631 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6651 0 68 62 6781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00376846
X-RAY DIFFRACTIONf_angle_d0.61299223
X-RAY DIFFRACTIONf_chiral_restr0.04111023
X-RAY DIFFRACTIONf_plane_restr0.00321200
X-RAY DIFFRACTIONf_dihedral_angle_d22.882609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.33981490.3162704X-RAY DIFFRACTION99.76
2.45-2.510.36451360.31452724X-RAY DIFFRACTION99.9
2.51-2.570.36551400.31552722X-RAY DIFFRACTION99.76
2.57-2.640.39721420.32112753X-RAY DIFFRACTION100
2.64-2.720.41231720.31682707X-RAY DIFFRACTION99.9
2.72-2.810.34081330.28782735X-RAY DIFFRACTION99.97
2.81-2.910.3091630.2572737X-RAY DIFFRACTION99.97
2.91-3.020.30211400.25872741X-RAY DIFFRACTION99.97
3.02-3.160.28931270.2532749X-RAY DIFFRACTION100
3.16-3.330.30191210.25112792X-RAY DIFFRACTION99.97
3.33-3.540.28531270.23382780X-RAY DIFFRACTION99.9
3.54-3.810.26911490.21592795X-RAY DIFFRACTION99.97
3.81-4.190.24141470.19332766X-RAY DIFFRACTION99.93
4.19-4.80.2141560.17512796X-RAY DIFFRACTION100
4.8-6.040.24431540.20552844X-RAY DIFFRACTION99.97
6.04-48.220.18941500.17992980X-RAY DIFFRACTION99.68
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)
15.98693024428-0.268163188433-0.07357253528890.160975963846-0.1474214767750.140641787876-0.0792369001483-0.8827983132030.4662174282060.3876603320580.0970175898451-0.519864508555-0.03576616972940.919293521393-0.02769308505071.203938710670.0393317140638-0.1973372318761.43388415026-0.2067139307811.17126940669-1.1760768057869.4404770235-23.9518132904
21.5580792206-0.732978779959-0.9383049412151.401664382031.401904073294.79716962788-0.190236059609-0.263742388398-0.06450941301390.2330215592640.1143591545610.0284048502741-0.00275834347153-0.02843288040740.0654701017640.48309218850.0471266282578-0.1247439927210.4135626001610.02041142783890.590666490021-27.461333132756.4289416497-36.0755401369
36.86928623019-2.16101441437-4.642020400361.417371965730.9415818869783.478110215570.214654289165-0.1354590523220.133596677697-0.643083633842-0.08728905234-0.572884186895-0.3981484544910.491238344947-0.1258052069680.805971461-0.2807568013150.1476369451051.01738988779-0.09514454408120.668974991947-27.90220361669.2105718812-7.33019371507
43.84214415995-0.5620565885911.895676429561.52147902713-0.3461243286693.60014554332-0.33957530466-0.8325089476050.2944033085670.2748145577140.0536847145092-0.0185501606305-0.651999832668-0.04260460494370.2688319127610.478669000406-0.0726990349146-0.06630535416420.626025786606-0.01821323038090.490507737045-2.8915431691718.9581159822-27.5313855104
58.76284097729-1.29804006828-1.249115385441.99999549423-0.2807565101032.00001406571-0.3952837726130.612536518903-0.6729297441890.169136538747-0.422506640455-0.362115360543.202265319911.647205269720.8160831790331.568880344170.1158492854730.01134475590711.547402252660.0962127376771.19591122453-34.720551583820.2402433267-10.0113935919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 458 through 573 )
2X-RAY DIFFRACTION2chain 'A' and (resid 574 through 878 )
3X-RAY DIFFRACTION3chain 'B' and (resid 458 through 573 )
4X-RAY DIFFRACTION4chain 'B' and (resid 574 through 878 )
5X-RAY DIFFRACTION5chain 'C' and (resid 156 through 158 )

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