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- PDB-6twx: MAGI1_2 complexed with a phosphorylated 16E6 peptide -

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Basic information

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


positive regulation of low-density lipoprotein particle receptor binding / symbiont-mediated suppression of host transcription / 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 low-density lipoprotein particle receptor binding / symbiont-mediated suppression of host transcription / 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 / positive regulation of receptor recycling / phosphatidylserine binding / 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 / cell periphery / PDZ domain binding / 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 / vesicle / protease binding / host cell cytoplasm / cell surface receptor signaling pathway / early endosome / cell adhesion / endosome / virus-mediated perturbation of host defense response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / lysosomal membrane / DNA-templated transcription / calcium ion binding / host cell nucleus / 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 / 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 / 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: 2.3 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id

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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: 16E6 peptide
D: 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,03420
Polymers98,8324
Non-polymers1,20116
Water2,630146
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
D: 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9019
Polymers49,4162
Non-polymers4857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-49 kcal/mol
Surface area20890 Å2
MethodPISA
2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
C: 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,13311
Polymers49,4162
Non-polymers7179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-55 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.470, 96.550, 198.520
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, 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 16E6 peptide


Mass: 1316.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16 / References: UniProt: P03126*PLUS

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Non-polymers , 4 types, 162 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3000, 100mM Na-citrate (5.5), 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: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47 Å / Num. obs: 52873 / % possible obs: 98.8 % / Redundancy: 27.1 % / Biso Wilson estimate: 54.89 Å2 / CC1/2: 1 / Net I/σ(I): 15.33
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 3833 / CC1/2: 0.561

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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: 2.3→46.91 Å / SU ML: 0.3397 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0603
RfactorNum. reflection% reflection
Rfree0.2592 2560 4.85 %
Rwork0.2092 --
obs0.2116 52781 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 80.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 62 146 6904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456858
X-RAY DIFFRACTIONf_angle_d0.67259237
X-RAY DIFFRACTIONf_chiral_restr0.04441027
X-RAY DIFFRACTIONf_plane_restr0.0041196
X-RAY DIFFRACTIONf_dihedral_angle_d23.3452615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.36271350.29992721X-RAY DIFFRACTION98.14
2.34-2.390.32021230.28462736X-RAY DIFFRACTION98.08
2.39-2.440.31171500.27612739X-RAY DIFFRACTION98.23
2.44-2.50.32071570.26442700X-RAY DIFFRACTION98.59
2.5-2.560.33011350.26612754X-RAY DIFFRACTION97.4
2.56-2.630.31951490.26822755X-RAY DIFFRACTION100
2.63-2.710.40021360.28162730X-RAY DIFFRACTION97.78
2.71-2.80.31751360.26622777X-RAY DIFFRACTION98.15
2.8-2.90.31211430.24682777X-RAY DIFFRACTION99.86
2.9-3.010.30681340.23782780X-RAY DIFFRACTION98.55
3.01-3.150.30691280.24112779X-RAY DIFFRACTION98.78
3.15-3.320.28651360.2352774X-RAY DIFFRACTION98.95
3.32-3.520.24461480.21962808X-RAY DIFFRACTION99.19
3.52-3.80.25381640.20072795X-RAY DIFFRACTION99.33
3.8-4.180.24591380.1812829X-RAY DIFFRACTION99.13
4.18-4.780.21611380.16732865X-RAY DIFFRACTION99.47
4.78-6.020.21241630.19332887X-RAY DIFFRACTION99.71
6.02-46.90.23431470.18013015X-RAY DIFFRACTION99
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)
11.250911760680.0769142292758-0.22874677799-0.00479166560776-0.03882234512470.05319354105840.0368522695062-0.6229816030770.1420054984190.2024075481780.0569558383274-0.6187875809350.06864279150680.81932627885-0.1540439399531.199488802470.0760478346486-0.1526152700721.45362544551-0.1893616292641.14361273669-1.4010464266769.8339617048-24.1656051027
21.36565227795-0.753082949273-0.2023847647941.079326815680.8032757107893.03979760802-0.174232588189-0.219306048021-0.04298561527290.210414091560.1154861933220.0433658217481-0.0457025599023-0.07223249639140.06302771304680.4283067320990.0450358421139-0.05371717646030.3493603208540.004381265648780.50663299627-27.605045263756.6999809658-36.3962460262
32.06654205507-0.634229436111-1.496251692590.352793430490.2027335863111.257433669720.05478193638360.01532237423560.154441687204-0.9340555803820.150953697691-0.525717779452-0.3686365571160.293846799698-0.194561400920.917605470078-0.3103129504560.2396126928991.04828046491-0.1369917143440.671229708818-28.10954072379.40210443535-7.34205383694
42.60234881803-0.1969380539181.011463820741.03151138145-0.2009112713492.10284121374-0.187714495927-0.6432340796640.223685462070.2184713639770.0250385794971-0.0144644754613-0.373667417523-0.05301519958650.158851588210.437162473741-0.0594925071395-0.02687387224170.526821273715-0.03602189582050.406045667156-3.0266798091119.2015383543-27.581189681
53.43323481932.41474920444-3.909831472763.85406577243-5.597776293128.21546638979-0.09467500826330.8260121926980.278918333369-0.6876658060780.326426214650.01812815239490.43156105159-0.68161879945-0.1549858615592.03345088228-0.1672845028470.188512579621.3453488689-0.03733049554721.13286314969-34.146054738420.6571006321-11.5419215242
62.000609506931.999520535911.999456453891.999926798511.999173417671.99997166818-1.026212905521.30541819952-0.471660978253-0.6416230473921.434715115580.9820526928861.61508802794-2.34118095043-0.3744036040861.67414516502-0.24205322307-0.01796604555761.95073864308-0.2976886682171.70712772883-0.051647905163160.9264461011-16.317959777
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 155 through 158 )
6X-RAY DIFFRACTION6chain 'D' and (resid 157 through 158 )

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