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- PDB-1gyv: Gamma-adaptin appendage domain from clathrin adaptor AP1, L762E mutant -

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Basic information

Entry
Database: PDB / ID: 1gyv
TitleGamma-adaptin appendage domain from clathrin adaptor AP1, L762E mutant
ComponentsADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
KeywordsENDOCYTOSIS / ADAPTOR / CLATHRIN / GOLGI / ADAPTIN
Function / homology
Function and homology information


basolateral protein secretion / Lysosome Vesicle Biogenesis / AP-1 adaptor complex / platelet dense granule organization / melanosome assembly / Golgi Associated Vesicle Biogenesis / MHC class II antigen presentation / clathrin-coated vesicle / vesicle-mediated transport / clathrin-coated pit ...basolateral protein secretion / Lysosome Vesicle Biogenesis / AP-1 adaptor complex / platelet dense granule organization / melanosome assembly / Golgi Associated Vesicle Biogenesis / MHC class II antigen presentation / clathrin-coated vesicle / vesicle-mediated transport / clathrin-coated pit / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / presynapse / 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 ...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: 1.71 Å
AuthorsEvans, P.R. / 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 1.4Oct 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 1.5Dec 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,4331
Polymers13,4331
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.720, 54.820, 67.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 13433.230 Da / Num. of mol.: 1 / Fragment: APPENDAGE DOMAIN, RESIDUES 703-821 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growpH: 7.4
Details: 50MM HEPES PH7.4,0.9M NA/K TARTRATE 20% W/V GLYCEROL, pH 7.40
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
550 mMHEPES1reservoirpH7.4
60.9 Msodium acetate1reservoir
720 %(w/v)glycerol1reservoir

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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: Jun 15, 2000 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 1.7→18.7 Å / Num. obs: 14209 / % possible obs: 99.6 % / Observed criterion σ(I): 6 / Redundancy: 6.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 6 / % possible all: 97.9
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

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

1gyu


Resolution: 1.71→42.64 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.005 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1408 10 %RANDOM
Rwork0.178 ---
obs0.182 12740 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.71→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 0 191 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022954
X-RAY DIFFRACTIONr_bond_other_d0.0010.02852
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.851.9371299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.86831997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021049
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02173
X-RAY DIFFRACTIONr_nbd_refined0.2280.3135
X-RAY DIFFRACTIONr_nbd_other0.2170.3849
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3930.5159
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0160.32
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.317
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4340.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3271.5605
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2822994
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1133349
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1584.5305
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 109
Rwork0.24 881
Refinement
*PLUS
Highest resolution: 1.7 Å / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

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