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- PDB-6qh6: AP2 clathrin adaptor core with two cargo peptides in open+ confor... -

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Basic information

Entry
Database: PDB / ID: 6qh6
TitleAP2 clathrin adaptor core with two cargo peptides in open+ conformation
Components
  • (AP-2 complex subunit ...) x 5
  • CD4 CARGO PEPTIDE
  • TGN38 CARGO PEPTIDE
KeywordsPROTEIN TRANSPORT / ENDOCYTOSIS / TRAFFICKING / CELL MEMBRANE
Function / homology
Function and homology information


Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / secretory vesicle / LDL clearance ...Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / secretory vesicle / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance / Retrograde neurotrophin signalling / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / VLDLR internalisation and degradation / MHC class II antigen presentation / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / Recycling pathway of L1 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / response to methamphetamine hydrochloride / Cargo recognition for clathrin-mediated endocytosis / maintenance of protein location in cell / cellular response to ionomycin / Cargo recognition for clathrin-mediated endocytosis / Recycling pathway of L1 / Retrograde neurotrophin signalling / T cell selection / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin coat assembly / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / LDL clearance / MHC class II protein binding / Clathrin-mediated endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / signal sequence binding / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / coronary vasculature development / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / Alpha-defensins / neurotransmitter secretion / endolysosome membrane / regulation of T cell activation / response to vitamin D / extracellular matrix structural constituent / aorta development / Other interleukin signaling / Neutrophil degranulation / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / T cell receptor complex / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / positive regulation of protein kinase activity / regulation of calcium ion transport / positive regulation of calcium ion transport into cytosol / macrophage differentiation / Generation of second messenger molecules / positive regulation of receptor internalization / immunoglobulin binding / positive regulation of endocytosis / T cell differentiation / Co-inhibition by PD-1 / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / Binding and entry of HIV virion
Similarity search - Function
AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit ...AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Immunoglobulin C2-set / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Immunoglobulin C2-set domain / Clathrin adaptor complexes medium chain signature 2. / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Armadillo-like helical / Immunoglobulin subtype / Immunoglobulin / Armadillo-type fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD4 / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu / AP-2 complex subunit mu / AP-2 complex subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
Bos taurus (domestic cattle)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsWrobel, A.G. / Owen, D.J. / McCoy, A.J. / Evans, P.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust090909/Z/09/Z United Kingdom
Wellcome Trust097040/Z/11/Z United Kingdom
CitationJournal: Dev.Cell / Year: 2019
Title: Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation.
Authors: Wrobel, A.G. / Kadlecova, Z. / Kamenicky, J. / Yang, J.C. / Herrmann, T. / Kelly, B.T. / McCoy, A.J. / Evans, P.R. / Martin, S. / Muller, S. / Sroubek, F. / Neuhaus, D. / Honing, S. / Owen, D.J.
History
DepositionJan 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP-2 complex subunit alpha
B: AP-2 complex subunit beta
M: AP-2 complex subunit mu
N: AP-2 complex subunit mu
P: TGN38 CARGO PEPTIDE
Q: CD4 CARGO PEPTIDE
S: AP-2 complex subunit sigma


Theoretical massNumber of molelcules
Total (without water)258,0647
Polymers258,0647
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16630 Å2
ΔGint-63 kcal/mol
Surface area73000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.500, 180.500, 210.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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AP-2 complex subunit ... , 5 types, 5 molecules ABMNS

#1: Protein AP-2 complex subunit alpha


Mass: 69642.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2a2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66HM2, UniProt: P18484*PLUS
#2: Protein AP-2 complex subunit beta / AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta ...AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta / Beta-2-adaptin / Beta-adaptin / Clathrin assembly protein complex 2 beta large chain / Plasma membrane adaptor HA2/AP2 adaptin beta subunit


Mass: 67091.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP2B1, ADTB2, CLAPB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63010
#3: 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 / HA2 50 kDa subunit / Mu2-adaptin / Plasma membrane adaptor AP-2 50 kDa protein


Mass: 51124.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: AP2M1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZC13
#4: 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: 51044.113 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
#7: Protein AP-2 complex subunit sigma / Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / ...Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / Clathrin assembly protein 2 sigma small chain / Clathrin coat assembly protein AP17 / Clathrin coat-associated protein AP17 / Plasma membrane adaptor AP-2 17 kDa protein / Sigma-adaptin 3b / Sigma2-adaptin


Mass: 17038.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2s1, Ap17, Claps2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62743

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Protein/peptide , 2 types, 2 molecules PQ

#5: Protein/peptide TGN38 CARGO PEPTIDE


Mass: 808.860 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: YXXPhi INTERNALISATION SIGNAL MOTIF / Source: (synth.) Homo sapiens (human)
#6: Protein/peptide CD4 CARGO PEPTIDE


Mass: 1314.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ACIDIC DILEUCINE INTERNALISATION SIGNAL MOTIF / Source: (synth.) Homo sapiens (human) / References: UniProt: P01730*PLUS

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Details

Has protein modificationY

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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: 3.31 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 7.5% PVA, 9% 1-propanol, 90 mM Hepes pH 7.4, 100 mM guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.252 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.252 Å / Relative weight: 1
ReflectionResolution: 5→91 Å / Num. obs: 15525 / % possible obs: 99.6 % / Redundancy: 4.8 % / CC1/2: 0.942 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.138 / Rrim(I) all: 0.247 / Net I/σ(I): 3.6
Reflection shellResolution: 5→5.59 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5→91 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.927 / SU B: 163.978 / SU ML: 1.636 / Cross valid method: THROUGHOUT / ESU R Free: 1.382
RfactorNum. reflection% reflectionSelection details
Rfree0.28519 742 4.8 %RANDOM
Rwork0.25915 ---
obs0.26043 14738 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 324.42 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20 Å2
2---2.05 Å20 Å2
3---4.1 Å2
Refinement stepCycle: 1 / Resolution: 5→91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13342 0 0 0 13342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913569
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.97218367
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70651661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.62224.33612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.367152497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9141589
X-RAY DIFFRACTIONr_chiral_restr0.1010.22136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110017
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it19.07131.776671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it32.36447.5978323
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it20.88533.1336895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined58.16653425
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 5→5.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 53 -
Rwork0.451 1061 -
obs--99.46 %

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