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- PDB-9ddt: AAGAB pseudoGTPase domain in complex with AP-1 clathrin adaptor c... -

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Basic information

Entry
Database: PDB / ID: 9ddt
TitleAAGAB pseudoGTPase domain in complex with AP-1 clathrin adaptor complex sigma 3 subunit
Components
  • AP-1 complex subunit sigma-3
  • Alpha- and gamma-adaptin-binding protein p34
KeywordsPROTEIN BINDING / Adaptin / Membrane trafficking / PROTEIN-protein interaction / pseudoGTPase
Function / homology
Function and homology information


AP-1 adaptor complex / platelet dense granule organization / melanosome assembly / clathrin adaptor activity / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein targeting / vesicle-mediated transport / clathrin-coated pit / MHC class II antigen presentation ...AP-1 adaptor complex / platelet dense granule organization / melanosome assembly / clathrin adaptor activity / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein targeting / vesicle-mediated transport / clathrin-coated pit / MHC class II antigen presentation / cytoplasmic vesicle membrane / Nef mediated downregulation of MHC class I complex cell surface expression / trans-Golgi network membrane / intracellular protein transport / protein transport / early endosome / nuclear speck / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / cytosol / cytoplasm
Similarity search - Function
Alpha/gamma-adaptin-binding protein p34 / Alpha and gamma adaptin binding protein p34 / AP-1 complex subunit sigma / Adaptor protein complex, sigma subunit / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Longin-like domain superfamily
Similarity search - Domain/homology
Alpha- and gamma-adaptin-binding protein p34 / AP-1 complex subunit sigma-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsWang, B. / Tian, Y. / Yin, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138685 United States
CitationJournal: To Be Published
Title: A pseudoGTPase mediates chaperone-substrate interaction in membrane trafficking complex assembly
Authors: Wang, B. / Tian, Y. / Yin, Q.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha- and gamma-adaptin-binding protein p34
B: AP-1 complex subunit sigma-3


Theoretical massNumber of molelcules
Total (without water)37,9812
Polymers37,9812
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-6 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.294, 61.608, 92.854
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 Alpha- and gamma-adaptin-binding protein p34


Mass: 19675.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAGAB / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PD74
#2: Protein AP-1 complex subunit sigma-3 / Adaptor protein complex AP-1 subunit sigma-1C / Adaptor-related protein complex 1 subunit sigma-1C ...Adaptor protein complex AP-1 subunit sigma-1C / Adaptor-related protein complex 1 subunit sigma-1C / 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: 18305.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP1S3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96PC3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH 6.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.68→46.43 Å / Num. obs: 33173 / % possible obs: 98.68 % / Redundancy: 12.9 % / Biso Wilson estimate: 26.2 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07416 / Rpim(I) all: 0.02136 / Rrim(I) all: 0.07728 / Net I/σ(I): 18.51
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 0.8291 / Num. unique obs: 3112 / CC1/2: 0.872

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→46.43 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 2000 6.01 %
Rwork0.1825 --
obs0.1843 33173 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 0 323 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072398
X-RAY DIFFRACTIONf_angle_d1.033250
X-RAY DIFFRACTIONf_dihedral_angle_d15.718309
X-RAY DIFFRACTIONf_chiral_restr0.066366
X-RAY DIFFRACTIONf_plane_restr0.006409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.24671220.22911912X-RAY DIFFRACTION86
1.72-1.760.23921410.21812186X-RAY DIFFRACTION98
1.76-1.820.24321410.2172220X-RAY DIFFRACTION99
1.82-1.870.23761430.2072231X-RAY DIFFRACTION99
1.87-1.940.24621430.19872233X-RAY DIFFRACTION99
1.94-2.020.2521430.19792236X-RAY DIFFRACTION99
2.02-2.110.2031430.18632250X-RAY DIFFRACTION99
2.11-2.220.22891410.18012203X-RAY DIFFRACTION99
2.22-2.360.1861440.18262254X-RAY DIFFRACTION100
2.36-2.540.24951460.20152262X-RAY DIFFRACTION100
2.54-2.80.22871460.19742291X-RAY DIFFRACTION100
2.8-3.20.21821440.18692238X-RAY DIFFRACTION98
3.2-4.040.17881480.16472317X-RAY DIFFRACTION100
4.04-46.430.20171550.16892426X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 37.528 Å / Origin y: 23.1299 Å / Origin z: 28.6707 Å
111213212223313233
T0.1704 Å20.0141 Å2-0.0286 Å2-0.1479 Å20.0069 Å2--0.166 Å2
L0.9962 °2-0.0867 °2-0.4769 °2-0.6324 °20.2813 °2--0.9306 °2
S-0.0153 Å °0.0152 Å °-0.0907 Å °-0.0254 Å °-0.0149 Å °0.0465 Å °0.0596 Å °-0.0089 Å °-0 Å °
Refinement TLS groupSelection details: all

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