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- PDB-1iu1: Crystal structure of human gamma1-adaptin ear domain -

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Basic information

Entry
Database: PDB / ID: 1iu1
TitleCrystal structure of human gamma1-adaptin ear domain
Componentsgamma1-adaptin
KeywordsENDOCYTOSIS / Coated pits
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / cargo adaptor activity / small GTPase binding => GO:0031267 / AP-1 adaptor complex / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Golgi to lysosome transport / Golgi to vacuole transport / clathrin-coated vesicle membrane / melanosome organization ...virus-mediated perturbation of host defense response => GO:0019049 / cargo adaptor activity / small GTPase binding => GO:0031267 / AP-1 adaptor complex / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Golgi to lysosome transport / Golgi to vacuole transport / clathrin-coated vesicle membrane / melanosome organization / GTP-dependent protein binding / clathrin adaptor activity / clathrin-coated vesicle / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / positive regulation of natural killer cell mediated cytotoxicity / kinesin binding / MHC class II antigen presentation / receptor-mediated endocytosis / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / intracellular protein transport / cytoplasmic vesicle membrane / recycling endosome / antigen processing and presentation of exogenous peptide antigen via MHC class II / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / Golgi apparatus / membrane / cytosol / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsNogi, T. / Shiba, Y. / Kawasaki, M. / Shiba, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Takatsu, H. / Nakayama, K. / Wakatsuki, S.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structural basis for the accessory protein recruitment by the gamma-adaptin ear domain.
Authors: Nogi, T. / Shiba, Y. / Kawasaki, M. / Shiba, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Takatsu, H. / Nakayama, K. / Wakatsuki, S.
History
DepositionFeb 19, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: gamma1-adaptin
B: gamma1-adaptin


Theoretical massNumber of molelcules
Total (without water)32,2712
Polymers32,2712
Non-polymers00
Water2,378132
1
A: gamma1-adaptin


Theoretical massNumber of molelcules
Total (without water)16,1351
Polymers16,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: gamma1-adaptin


Theoretical massNumber of molelcules
Total (without water)16,1351
Polymers16,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.132, 62.132, 147.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein gamma1-adaptin / adapter-related protein complex 1 gamma 1 subunit


Mass: 16135.265 Da / Num. of mol.: 2 / Fragment: ear domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O43747
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4000, magnesium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
220 %(w/v)PEG40001drop
3200 mM1dropMgCl2
4100 mMHEPES-Na1droppH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.9
SYNCHROTRONPhoton Factory BL-6A30.96, 0.9778, 0.9785
Detector
TypeIDDetectorDate
OXFORD PX2101CCDSep 18, 2001
OXFORD PX2102CCDSep 18, 2001
ADSC QUANTUM 43CCDDec 12, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.961
30.97781
40.97851
ReflectionResolution: 1.8→57 Å / Num. all: 27518 / Num. obs: 27518 / % possible obs: 99.2 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.89 Å / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 372969 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.849 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24764 1363 5 %RANDOM
Rwork0.22649 ---
obs0.22756 26023 98.86 %-
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: 24.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 0 132 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221936
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9422633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1233241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20915365
X-RAY DIFFRACTIONr_chiral_restr0.0870.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021444
X-RAY DIFFRACTIONr_nbd_refined0.210.3798
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.5255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.321
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.59
X-RAY DIFFRACTIONr_mcbond_it0.8361.51223
X-RAY DIFFRACTIONr_mcangle_it1.6122007
X-RAY DIFFRACTIONr_scbond_it2.3243713
X-RAY DIFFRACTIONr_scangle_it4.0884.5626
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 94
Rwork0.269 1884
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Rfactor obs: 0.22756 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.33
LS refinement shell
*PLUS
Lowest resolution: 1.85 Å / Rfactor Rfree: 0.321 / Rfactor Rwork: 0.269

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