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- PDB-1w63: AP1 clathrin adaptor core -

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Basic information

Entry
Database: PDB / ID: 1w63
TitleAP1 clathrin adaptor core
Components
  • ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
  • ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
  • ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT
  • ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
KeywordsENDOCYTOSIS / CLATHRIN ADAPTOR / TRANSPORT / COATED PITS
Function / homology
Function and homology information


basolateral protein secretion / synaptic vesicle budding from endosome / clathrin coat / Lysosome Vesicle Biogenesis / positive regulation of natural killer cell degranulation / AP-1 adaptor complex / endosome to melanosome transport / Lysosome Vesicle Biogenesis / platelet dense granule organization / clathrin adaptor complex ...basolateral protein secretion / synaptic vesicle budding from endosome / clathrin coat / Lysosome Vesicle Biogenesis / positive regulation of natural killer cell degranulation / AP-1 adaptor complex / endosome to melanosome transport / Lysosome Vesicle Biogenesis / platelet dense granule organization / clathrin adaptor complex / melanosome assembly / MHC class II antigen presentation / Golgi to lysosome transport / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / clathrin-coated vesicle membrane / clathrin coat assembly / clathrin-cargo adaptor activity / MHC class II antigen presentation / melanosome organization / GTP-dependent protein binding / positive regulation of natural killer cell mediated cytotoxicity / determination of left/right symmetry / retrograde transport, endosome to Golgi / clathrin-coated vesicle / clathrin binding / synaptic vesicle endocytosis / kinesin binding / collagen binding / vesicle-mediated transport / Neutrophil degranulation / clathrin-coated pit / protein serine/threonine kinase binding / trans-Golgi network membrane / intracellular protein transport / kidney development / trans-Golgi network / recycling endosome / small GTPase binding / response to virus / terminal bouton / synaptic vesicle / presynapse / heart development / early endosome / lysosomal membrane / synapse / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / cytosol
Similarity search - Function
Beta-Lactamase - #60 / AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / 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-Lactamase - #60 / AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / 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 / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / AP complex subunit beta / Clathrin adaptor complexes medium chain signature 1. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / 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 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / TBP domain superfamily / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Beta-Lactamase / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-1 / AP-1 complex subunit beta-1 / AP-1 complex subunit sigma-1A
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsHeldwein, E. / Macia, E. / Wang, J. / Yin, H.L. / Kirchhausen, T. / Harrison, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal Structure of the Clathrin Adaptor Protein 1 Core
Authors: Heldwein, E. / Macia, E. / Wang, J. / Yin, H.L. / Kirchhausen, T. / Harrison, S.C.
History
DepositionAug 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector / _entity_src_gen.pdbx_host_org_vector_type / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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

Downloads & links

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Assembly

Deposited unit
A: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
B: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
C: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
D: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
E: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
F: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
G: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
H: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
I: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
J: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
K: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
L: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
M: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
N: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
O: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
P: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
Q: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT
R: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
S: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT
T: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT
U: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT
V: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
W: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT
X: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT


Theoretical massNumber of molelcules
Total (without water)1,218,98324
Polymers1,218,98324
Non-polymers00
Water00
1
A: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
B: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
M: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
S: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT


Theoretical massNumber of molelcules
Total (without water)203,1644
Polymers203,1644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
D: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
N: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
T: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT


Theoretical massNumber of molelcules
Total (without water)203,1644
Polymers203,1644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
F: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
O: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
U: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT


Theoretical massNumber of molelcules
Total (without water)203,1644
Polymers203,1644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
I: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
J: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
R: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
X: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT


Theoretical massNumber of molelcules
Total (without water)203,1644
Polymers203,1644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
K: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
L: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
V: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
W: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT


Theoretical massNumber of molelcules
Total (without water)203,1644
Polymers203,1644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
G: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
H: ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
P: ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
Q: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT


Theoretical massNumber of molelcules
Total (without water)203,1644
Polymers203,1644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)178.140, 178.140, 1134.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein
ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT / GAMMA-ADAPTIN / ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-1 SUBUNIT / GOLGI ADAPTOR HA1/AP1 ADAPTIN GAMMA- ...GAMMA-ADAPTIN / ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-1 SUBUNIT / GOLGI ADAPTOR HA1/AP1 ADAPTIN GAMMA-1 SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN


Mass: 69728.781 Da / Num. of mol.: 6 / Fragment: CORE, RESIDUES 0-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC1, PFASTBACHTB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P22892
#2: Protein
ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT / BETA-ADAPTIN 1 / ADAPTOR PROTEIN COMPLEX AP-1 BETA-1 SUBUNIT / GOLGI ADAPTOR HA1/AP1 ADAPTIN BETA ...BETA-ADAPTIN 1 / ADAPTOR PROTEIN COMPLEX AP-1 BETA-1 SUBUNIT / GOLGI ADAPTOR HA1/AP1 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 BETA LARGE CHAIN


Mass: 66086.398 Da / Num. of mol.: 6 / Fragment: CORE, RESIDUE 1-584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PFASTBAC1, PFASTBACHTB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P52303
#3: Protein
ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT / MU-ADAPTIN 1 / ADAPTOR PROTEIN COMPLEX AP-1 MU-1 SUBUNIT / GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 ...MU-ADAPTIN 1 / ADAPTOR PROTEIN COMPLEX AP-1 MU-1 SUBUNIT / GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 SUBUNIT / CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 1 / CLATHRIN COAT ASSEMBLY PROTEIN AP47 / CLATHRIN COAT ASSOCIATED PROTEIN AP47 / AP-MU CHAIN FAMILY MEMBER MU1A


Mass: 48590.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC1, PFASTBACHTB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35585
#4: Protein
ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT / SIGMA-ADAPTIN 1A / ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1A SUBUNIT / GOLGI ADAPTOR HA1/AP1 ADAPTIN ...SIGMA-ADAPTIN 1A / ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1A SUBUNIT / GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1A SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA-1A SMALL CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP19 / HA1 19 KDA SUBUNIT / SIGMA 1A SUBUNIT OF AP-1 CLATHRIN


Mass: 18757.994 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC1, PFASTBACHTB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61967
Sequence detailsFIRST 5 RESIDUES (GAGMS) OF CHAIN A ORIGINATE FROM EXPRESSION VECTOR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 70.97 %
Description: DATA WERE COLLECTED USING DOUBLE CCD DETECTOR SETUP
Crystal growpH: 7
Details: 8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.1808
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 4.01→39.84 Å / Num. obs: 141015 / % possible obs: 81.3 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.4
Reflection shellResolution: 4→4.1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 69.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GW5

1gw5
PDB Unreleased entry


Resolution: 4→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: CHAIN A IS MISSING RESIDUES 590-613 CHAIN B IS MISSING RESIDUES 1, 268-274, AND 584 CHAIN M IS MISSING RESIDUES 1, 146-156, 219-231, AND 363-372 CHAIN S IS MISSING RESIDUES 149-158
RfactorNum. reflection% reflectionSelection details
Rfree0.3097 6890 3.9 %THIN RESOLUTION SHELLS
Rwork0.2972 ---
obs0.2972 137671 78.8 %-
Solvent computationBsol: 41.3296 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.719 Å2-24.176 Å20 Å2
2---4.719 Å20 Å2
3---9.439 Å2
Refinement stepCycle: LAST / Resolution: 4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81744 0 0 0 81744
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.86103
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM

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