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- PDB-1hes: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1hes
TitleMU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH P-selectin INTERNALIZATION PEPTIDE SHLGTYGVFTNAA
Components
  • CLATHRIN COAT ASSEMBLY PROTEIN AP50
  • P-SELECTIN PEPTIDE
KeywordsENDOCYTOSIS/EXOCYTOSIS / ENDOCYTOSIS / ADAPTOR / PEPTIDE COMPLEX / PEPTIDE BINDING PROTE / ENDOCYTOSIS-EXOCYTOSIS complex
Function / homology
Function and homology information


regulation of integrin activation / Gap junction degradation / Formation of annular gap junctions / fucose binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / glycosphingolipid binding ...regulation of integrin activation / Gap junction degradation / Formation of annular gap junctions / fucose binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / glycosphingolipid binding / positive regulation of leukocyte tethering or rolling / platelet dense granule membrane / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / sialic acid binding / oligosaccharide binding / 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 / Clathrin-mediated endocytosis / calcium-dependent cell-cell adhesion / platelet alpha granule membrane / vesicle budding from membrane / clathrin-dependent endocytosis / leukocyte tethering or rolling / signal sequence binding / positive regulation of platelet activation / positive regulation of leukocyte migration / heterophilic cell-cell adhesion / low-density lipoprotein particle receptor binding / leukocyte cell-cell adhesion / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / vesicle-mediated transport / clathrin-coated pit / response to cytokine / Cell surface interactions at the vascular wall / intracellular protein transport / lipopolysaccharide binding / cell-cell adhesion / receptor internalization / integrin binding / endocytosis / terminal bouton / disordered domain specific binding / calcium-dependent protein binding / synaptic vesicle / Platelet degranulation / heparin binding / protein-containing complex assembly / cytoplasmic vesicle / response to lipopolysaccharide / defense response to Gram-negative bacterium / transmembrane transporter binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / cell adhesion / inflammatory response / external side of plasma membrane / calcium ion binding / synapse / lipid binding / glutamatergic synapse / extracellular space / plasma membrane
Similarity search - Function
Selectin superfamily / Selectin, C-type lectin-like domain / Mu homology domain, subdomain B / : / 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. ...Selectin superfamily / Selectin, C-type lectin-like domain / Mu homology domain, subdomain B / : / 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 / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
P-selectin / AP-2 complex subunit mu / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOwen, D.J. / Evans, P.R. / Green, S.A.
Citation
Journal: Traffic / Year: 2001
Title: A Third Specificity-Determining Site in Mu 2 Adaptin for Sequences Upstream of Yxx Phi Sorting Motifs
Authors: Owen, D.J. / Setiadi, H. / Evans, P.R. / Mcever, R.P. / Green, S.A.
#1: Journal: Science / Year: 1998
Title: A Structural Explanation for the Recognition of Tyrosine-Based Endocytotic Signals
Authors: Owen, D.J. / Evans, P.R.
History
DepositionNov 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLATHRIN COAT ASSEMBLY PROTEIN AP50
P: P-SELECTIN PEPTIDE


Theoretical massNumber of molelcules
Total (without water)34,6402
Polymers34,6402
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11.8 kcal/mol
Surface area17470 Å2
MethodPQS
Unit cell
Length a, b, c (Å)125.720, 125.720, 75.270
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 CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT ASSOCIATED PROTEIN AP50 / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / HA2 50 KDA ...CLATHRIN COAT ASSOCIATED PROTEIN AP50 / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / HA2 50 KDA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN / AP-2 MU 2 CHAIN / MU2 ADAPTIN


Mass: 32758.363 Da / Num. of mol.: 1 / Fragment: INTERNALIZATION SIGNAL BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE FIRST SEVEN RESIDUES OF THE POLYMER MAKE UP A HIS-TAG
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Gene: AP50 / Plasmid: PMW172H6 / Gene (production host): AP50 / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P20172, UniProt: P84092*PLUS
#2: Protein/peptide P-SELECTIN PEPTIDE


Mass: 1882.015 Da / Num. of mol.: 1 / Fragment: INTERNALIZATION SIGNAL / Source method: obtained synthetically
Details: PEPTIDE INTERNALISATION SIGNAL MOTIF FROM P-SELECTIN SHLGTYGVFTNAAFDPSP
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P16109
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 5.7 Å3/Da / Density % sol: 79 % / Description: ISOMORPHOUS TO 1BW8
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16 DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / Details: Owen, D.J., (1998) Science, 282, 1327. / PH range low: 7.1 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
22.2 M1reservoirNaCl
30.4 Msodium potassium phosphate1reservoir
410 mMdithiothreitol1reservoir
515 %(v/v)glycerol1reservoir
60.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.877
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2000 / Details: MIRROR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.877 Å / Relative weight: 1
ReflectionResolution: 3→22 Å / Num. obs: 13729 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 9.2 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 17.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.0106 / Mean I/σ(I) obs: 2 / Rsym value: 0.0106 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BW8

1bw8


Resolution: 3→100 Å / SU B: 18.91 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.442 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 671 4.9 %RANDOM
Rwork0.21 ---
obs0.213 13045 99.9 %-
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 0 33 2138
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONp_bond_d0.030.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.3481.968

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