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- PDB-1gyw: Gamma-adaptin appendage domain from clathrin adaptor AP1 A753D mutant -

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Basic information

Entry
Database: PDB / ID: 1gyw
TitleGamma-adaptin appendage domain from clathrin adaptor AP1 A753D mutant
ComponentsADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
KeywordsENDOCYTOSIS / ADAPTOR / COATED PITS
Function / homology
Function and homology information


basolateral protein secretion / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / melanosome assembly / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / MHC class II antigen presentation / clathrin-coated vesicle ...basolateral protein secretion / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / melanosome assembly / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / MHC class II antigen presentation / clathrin-coated vesicle / clathrin-coated pit / vesicle-mediated transport / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / early endosome / lysosomal membrane / perinuclear region of cytoplasm
Similarity search - Function
Gamma-adaptin ear (GAE) domain / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / 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 ...Gamma-adaptin ear (GAE) domain / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / 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 / Armadillo-like helical / Armadillo-type fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
AP-1 complex subunit gamma-1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEvans, P.R. / Miele, A.E. / Owen, D.J. / McMahon, H.M. / Kent, H.M.
CitationJournal: Structure / Year: 2002
Title: Gamma-adaptin appendage domain: structure and binding site for Eps15 and gamma-synergin.
Authors: Kent, H.M. / McMahon, H.T. / Evans, P.R. / Benmerah, A. / Owen, D.J.
History
DepositionApr 30, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _pdbx_database_status.status_code_sf
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
B: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5463
Polymers28,5102
Non-polymers351
Water3,207178
1
A: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2912
Polymers14,2551
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)14,2551
Polymers14,2551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.155, 62.155, 148.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.134391, 0.511664, 0.84861), (0.965782, 0.124069, -0.227754), (-0.22182, 0.85018, -0.477482)
Vector: 2.316, -34.029, 28.275)

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Components

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


Mass: 14255.128 Da / Num. of mol.: 2 / Fragment: APPENDAGE DOMAIN, RESIDUES 694-821 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX 4T2 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P22892
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.52 Å3/Da / Density % sol: 55.9 %
Crystal growMethod: vapor diffusion / pH: 8
Details: 24% PEG4000, 100 MM TRIS PH 8.0, 200MM MGCL2, VAPOUR DIFFUSION
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mMHEPES1drop
250 mM1dropNaCl
34 mMdithiothreitol1drop
45 mg/mlprotein1drop
524 %PEG40001reservoir
6100 mMTris1reservoirpH8.0
7200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54182
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2.4→23.06 Å / Num. obs: 11979 / % possible obs: 99.3 % / Observed criterion σ(I): 6 / Redundancy: 13.62 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.1922
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 13.41 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.18 / % possible all: 96.3

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE 1GYU

1gyu


Resolution: 2.4→57.74 Å / SU B: 7.025 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R Free: 0.288 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.26871 565 4.7 %RANDOM
Rwork0.19034 ---
obs-11374 99.35 %-
Displacement parametersBiso mean: 27.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 1 178 2172
LS refinement shell
*PLUS
Highest resolution: 2.404 Å / Lowest resolution: 2.467 Å / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.235 / Total num. of bins used: 20

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