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- PDB-1e42: Beta2-adaptin appendage domain, from clathrin adaptor AP2 -

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Basic information

Entry
Database: PDB / ID: 1.0E+42
TitleBeta2-adaptin appendage domain, from clathrin adaptor AP2
ComponentsAP-2 COMPLEX SUBUNIT BETA
KeywordsENDOCYTOSIS / ADAPTOR
Function / homology
Function and homology information


Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling ...Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / clathrin coat assembly / LDL clearance / clathrin-dependent endocytosis / signal sequence binding / coronary vasculature development / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / endolysosome membrane / neurotransmitter secretion / aorta development / ventricular septum development / clathrin binding / Recycling pathway of L1 / positive regulation of endocytosis / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / intracellular protein transport / kidney development / clathrin-coated endocytic vesicle membrane / cytoplasmic side of plasma membrane / synaptic vesicle / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / Potential therapeutics for SARS / protein-containing complex binding / glutamatergic synapse / membrane / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin-like - #1150 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain ...Immunoglobulin-like - #1150 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / 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 / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TATA-Binding Protein / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DITHIANE DIOL / NICKEL (II) ION / AP-2 complex subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsOwen, D.J. / Evans, P.R. / McMahon, H.T.
CitationJournal: Embo J. / Year: 2000
Title: The Structure and Function of the Beta2-Adaptin Appendage Domain
Authors: Owen, D.J. / Vallis, Y. / Pearse, B.M.F. / Mcmahon, H.T. / Evans, P.R.
History
DepositionJun 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP-2 COMPLEX SUBUNIT BETA
B: AP-2 COMPLEX SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,96315
Polymers58,1772
Non-polymers78613
Water14,808822
1
A: AP-2 COMPLEX SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4286
Polymers29,0881
Non-polymers3405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AP-2 COMPLEX SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5359
Polymers29,0881
Non-polymers4478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.040, 124.590, 67.640
Angle α, β, γ (deg.)90.00, 124.18, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.379985, 0.020033, -0.924776), (-0.011062, -0.999792, -0.017113), (-0.924927, 0.003727, 0.380127)
Vector: 4.137, 50.052, -5.467)
DetailsTHE BETA-ADAPTIN PROTEIN IS PART OF THE ASSEMBLY PROTEINCOMPLEX 2, (AP-2), THAT IS A HETEROTETRAMER COMPOSED OF TWO LARGE CHAINS (ALPHA AND BETA), A MEDIUM CHAIN (AP50)AND A SMALL CHAIN (AP17).

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AP-2 COMPLEX SUBUNIT BETA / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA ...PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN / AP105B / BETA2-ADAPTIN / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT BETA


Mass: 29088.453 Da / Num. of mol.: 2 / Fragment: APPENDAGE DOMAIN, RESIDUES 701-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P63010

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Non-polymers , 6 types, 835 molecules

#2: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCLONING HEADER MGSSHHHHHHSSGLVPRGSHM THEN RESIDUE 701-937

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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: 2.9 Å3/Da / Density % sol: 55 %
Crystal growpH: 8.8
Details: WELL SOLUTION: 1.6 - 2.0M MGCL2, 0.1M BICINE PH 8.7 - 9.0, 15% GLYCEROL, 1MM DTT. PROTEIN: 40MG/ML, 5MM HEPES, 50MM NACL, 4MM DTT, 1:1 MIXTURE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 8.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mMHEPES1drop
250 mM1dropNaCl
34 mMdithiothreitol1drop
440 mg/mlprotein1drop
51.6-2.0 M1reservoirMgCl2
60.1 MBicine1reservoirpH8.7-9.0
715 %(v/v)glycerol1reservoir
810 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Sep 15, 1998
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.7→19.96 Å / Num. obs: 71562 / % possible obs: 98.4 % / Observed criterion σ(I): 4 / Redundancy: 6.85 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/σ(I): 11.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.48 / Rsym value: 0.75 / % possible all: 89.6
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→67.42 Å / SU B: 3.538 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.164
Details: RESIDUES A980 AND B980 WERE MODELLED AS GLYCEROL, BUT IDENTIFICATION IS NOT CERTAIN. RESIDUE B970 WAS MODELLED AS A 50% NI ION, SINCE IT IS BOUND TO A HISTIDINE, BUT IT MAY BE ANOTHER MG ION
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3621 5.057 %RANDOM
Rwork0.196 ---
obs-67980 98.3 %-
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å20.8 Å2
2---2.4 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 37 822 4555
Software
*PLUS
Name: REFMAC / Version: VERSION 5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_deg1.9

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