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- PDB-9uuk: Crystal structure of the mu2 subunit of the clathrin-adaptor prot... -

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Basic information

Entry
Database: PDB / ID: 9uuk
TitleCrystal structure of the mu2 subunit of the clathrin-adaptor protein 2 (AP2) bound to HPV16 E7(residues 22-32; S31E and S32E)
Components
  • AP-2 complex subunit mu
  • Protein E7
KeywordsENDOCYTOSIS / mu2 / clathrin-adaptor protein 2 / AP2 / HPV16 / E7 / CR2
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated suppression of host cGAS-STING signal transduction / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / symbiont-mediated perturbation of host transcription / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated suppression of host cGAS-STING signal transduction / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / symbiont-mediated perturbation of host transcription / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / symbiont-mediated perturbation of host cell cycle progression / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of vesicle size / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / symbiont-mediated suppression of host apoptosis / Clathrin-mediated endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / low-density lipoprotein particle receptor binding / positive regulation of actin filament polymerization / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / viral process / negative regulation of protein localization to plasma membrane / clathrin-coated pit / intracellular protein transport / receptor internalization / terminal bouton / disordered domain specific binding / synaptic vesicle / protein-containing complex assembly / cytoplasmic vesicle / DNA-binding transcription factor binding / transmembrane transporter binding / host cell cytoplasm / postsynapse / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA-binding transcription factor activity / protein domain specific binding / DNA-templated transcription / lipid binding / synapse / host cell nucleus / glutamatergic synapse / DNA binding / zinc ion binding / plasma membrane
Similarity search - Function
Papillomavirus E7 / E7 protein, Early protein / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit ...Papillomavirus E7 / E7 protein, Early protein / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily
Similarity search - Domain/homology
Protein E7 / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Human papillomavirus 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.199 Å
AuthorsKu, B. / Jung, S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00278696 Korea, Republic Of
National Research Foundation (NRF, Korea)KGM9952522 Korea, Republic Of
National Research Foundation (NRF, Korea)KGM1322511 Korea, Republic Of
CitationJournal: J.Microbiol / Year: 2025
Title: Crystal structures of the mu 2 subunit of clathrin-adaptor protein 2 in complex with peptides derived from human papillomavirus 16 E7.
Authors: Jung, S. / Lim, D. / Choi, J.S. / Shin, H.C. / Kim, S.J. / Ku, B.
History
DepositionMay 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-2 complex subunit mu
B: Protein E7


Theoretical massNumber of molelcules
Total (without water)33,5432
Polymers33,5432
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-4 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.206, 125.206, 73.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein AP-2 complex subunit mu / AP-2 mu chain / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit ...AP-2 mu chain / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit mu / Clathrin assembly protein complex 2 mu medium chain / Clathrin coat assembly protein AP50 / Clathrin coat-associated protein AP50 / Mu2-adaptin / Plasma membrane adaptor AP-2 50 kDa protein


Mass: 32124.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84092
#2: Protein/peptide Protein E7


Mass: 1418.482 Da / Num. of mol.: 1 / Mutation: S31E, S32E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus 16 / Gene: E7 / Production host: synthetic construct (others) / References: UniProt: P03129
Has protein modificationN

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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: 4.96 Å3/Da / Density % sol: 75.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.5 M sodium chloride and 100 mM potassium phosphate monobasic/sodium phosphate dibasic (pH 6.2)

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.199→50 Å / Num. obs: 10719 / % possible obs: 97.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.5
Reflection shellResolution: 3.199→3.26 Å / Rmerge(I) obs: 0.367 / Num. unique obs: 522

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.199→35.794 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 1081 10.09 %
Rwork0.2054 --
obs0.2092 10714 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.199→35.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 0 0 1940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111977
X-RAY DIFFRACTIONf_angle_d1.2132666
X-RAY DIFFRACTIONf_dihedral_angle_d16.3241218
X-RAY DIFFRACTIONf_chiral_restr0.068301
X-RAY DIFFRACTIONf_plane_restr0.006335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.199-3.34410.33011350.311174X-RAY DIFFRACTION96
3.3441-3.52030.27821320.25311199X-RAY DIFFRACTION97
3.5203-3.74060.27221280.21861181X-RAY DIFFRACTION98
3.7406-4.0290.24641400.20991220X-RAY DIFFRACTION98
4.029-4.43380.23651290.17871177X-RAY DIFFRACTION97
4.4338-5.07390.17471370.15761225X-RAY DIFFRACTION99
5.0739-6.38660.23031330.21441221X-RAY DIFFRACTION98
6.3866-35.7940.27061470.20811236X-RAY DIFFRACTION98

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