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- PDB-4hmy: Structural basis for recruitment and activation of the AP-1 clath... -

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Basic information

Entry
Database: PDB / ID: 4hmy
TitleStructural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1
Components
  • (AP-1 complex subunit ...) x 4
  • ADP-ribosylation factor 1
KeywordsPROTEIN TRANSPORT / protein trafficking / Arf1 GTPase activation / Arf1 GTPase binding / Trans-Golgi membrane
Function / homology
Function and homology information


basolateral protein secretion / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / platelet dense granule organization / Glycosphingolipid transport / melanosome assembly / regulation of receptor internalization ...basolateral protein secretion / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / platelet dense granule organization / Glycosphingolipid transport / melanosome assembly / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Golgi Associated Vesicle Biogenesis / Synthesis of PIPs at the Golgi membrane / clathrin adaptor activity / MHC class II antigen presentation / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / determination of left/right symmetry / clathrin-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / clathrin binding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Synthesis of PIPs at the plasma membrane / cell leading edge / intracellular copper ion homeostasis / protein targeting / COPI-mediated anterograde transport / vesicle-mediated transport / clathrin-coated pit / Neutrophil degranulation / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoplasmic vesicle membrane / Nef mediated downregulation of MHC class I complex cell surface expression / sarcomere / trans-Golgi network membrane / small monomeric GTPase / intracellular protein transport / kidney development / trans-Golgi network / cellular response to virus / synaptic vesicle / presynapse / heart development / early endosome / neuron projection / postsynaptic density / Golgi membrane / protein domain specific binding / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / synapse / protein kinase binding / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / Golgi apparatus / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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 / ADP-ribosylation factor 1-5 / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / 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 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-1 / ADP-ribosylation factor 1 / AP-1 complex subunit beta-1 / AP-1 complex subunit sigma-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsRen, X. / Farias, G.G. / Canagarajah, B.J. / Bonifacino, J.S. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Structural Basis for Recruitment and Activation of the AP-1 Clathrin Adaptor Complex by Arf1.
Authors: Ren, X. / Farias, G.G. / Canagarajah, B.J. / Bonifacino, J.S. / Hurley, J.H.
History
DepositionOct 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_ref_seq_dif.details / _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-1 complex subunit gamma-1
B: AP-1 complex subunit beta-1
M: AP-1 complex subunit mu-1
S: AP-1 complex subunit sigma-3
C: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,7537
Polymers221,2055
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)267.500, 267.500, 191.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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AP-1 complex subunit ... , 4 types, 4 molecules ABMS

#1: Protein AP-1 complex subunit gamma-1 / Adapter-related protein complex 1 subunit gamma-1 / Adaptor protein complex AP-1 subunit gamma-1 / ...Adapter-related protein complex 1 subunit gamma-1 / Adaptor protein complex AP-1 subunit gamma-1 / Clathrin assembly protein complex 1 gamma-1 large chain / Gamma-adaptin / Gamma1-adaptin / Golgi adaptor HA1/AP1 adaptin subunit gamma-1


Mass: 68194.094 Da / Num. of mol.: 1 / Fragment: UNP residues 1-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adtg, Ap1g1, Clapg1 / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P22892
#2: Protein AP-1 complex subunit beta-1 / Adapter-related protein complex 1 subunit beta-1 / Adaptor protein complex AP-1 subunit beta-1 / ...Adapter-related protein complex 1 subunit beta-1 / Adaptor protein complex AP-1 subunit beta-1 / Beta-1-adaptin / Beta-adaptin 1 / Clathrin assembly protein complex 1 beta large chain / Golgi adaptor HA1/AP1 adaptin beta subunit


Mass: 66186.562 Da / Num. of mol.: 1 / Fragment: UNP residues 1-584 / Mutation: I488F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADTB1, AP1B1, BAM22, CLAPB2 / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: Q10567
#3: Protein AP-1 complex subunit mu-1 / AP-mu chain family member mu1A / Adaptor protein complex AP-1 mu-1 subunit / Adaptor-related ...AP-mu chain family member mu1A / Adaptor protein complex AP-1 mu-1 subunit / Adaptor-related protein complex 1 mu-1 subunit / Clathrin assembly protein complex 1 medium chain 1 / Clathrin coat assembly protein AP47 / Clathrin coat-associated protein AP47 / Golgi adaptor HA1/AP1 adaptin mu-1 subunit / Mu-adaptin 1 / Mu1A-adaptin


Mass: 48606.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1m1, Cltnm / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P35585
#4: Protein AP-1 complex subunit sigma-3 / Adapter-related protein complex 1 sigma-1C subunit / Adaptor protein complex AP-1 sigma-1C subunit ...Adapter-related protein complex 1 sigma-1C subunit / Adaptor protein complex AP-1 sigma-1C subunit / Clathrin assembly protein complex 1 sigma-1C small chain / Golgi adaptor HA1/AP1 adaptin sigma-1C subunit / Sigma 1C subunit of AP-1 clathrin / Sigma-adaptin 1C / Sigma1C-adaptin


Mass: 18321.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP1S3 / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: Q96PC3

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Protein , 1 types, 1 molecules C

#5: Protein ADP-ribosylation factor 1


Mass: 19896.678 Da / Num. of mol.: 1 / Fragment: UNP residues 17-181 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Plasmid: pHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P84077

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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

Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M lithium sulfate, 0.1M Tris pH 8.5, 0.2M lithium nitrate, 0.7M ammonium sulphate, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 12, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7→50 Å / Num. all: 12533 / Num. obs: 12321 / % possible obs: 98.7 % / Observed criterion σ(F): 25 / Observed criterion σ(I): 1.9 / Redundancy: 7.1 % / Rsym value: 0.158
Reflection shellResolution: 7→7.12 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.9 / % possible all: 94.4

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XA7

2xa7


Resolution: 7→20 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 562 RANDOM
Rwork0.2 --
obs0.2 11117 -
all-12533 -
Refinement stepCycle: LAST / Resolution: 7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14710 0 33 0 14743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0033
X-RAY DIFFRACTIONc_angle_deg0.95
LS refinement shellResolution: 7→7.24 Å
RfactorNum. reflection% reflection
Rfree0.447 40 -
Rwork0.359 --
obs-955 81 %

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