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- PDB-9dds: Crystal structure of human AAGAB G domain with E144K mutation -

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Basic information

Entry
Database: PDB / ID: 9dds
TitleCrystal structure of human AAGAB G domain with E144K mutation
ComponentsAlpha- and gamma-adaptin-binding protein p34
KeywordsPROTEIN BINDING / Adaptin / Complex / Membrane transfer
Function / homologyAlpha/gamma-adaptin-binding protein p34 / Alpha and gamma adaptin binding protein p34 / protein transport / nuclear speck / cytoplasm / cytosol / Alpha- and gamma-adaptin-binding protein p34
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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: Alpha- and gamma-adaptin-binding protein p34


Theoretical massNumber of molelcules
Total (without water)39,3512
Polymers39,3512
Non-polymers00
Water6,630368
1
A: Alpha- and gamma-adaptin-binding protein p34

B: Alpha- and gamma-adaptin-binding protein p34


Theoretical massNumber of molelcules
Total (without water)39,3512
Polymers39,3512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area1360 Å2
ΔGint-6 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.268, 94.349, 102.796
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: 19675.293 Da / Num. of mol.: 2 / Fragment: G domain / Mutation: E144K
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH5.5, 29% 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: 0.99228 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99228 Å / Relative weight: 1
ReflectionResolution: 1.78→45.14 Å / Num. obs: 34572 / % possible obs: 93 % / Redundancy: 9.6 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.125 / Net I/σ(I): 14.4
Reflection shellResolution: 1.78→1.844 Å / Rmerge(I) obs: 0.841 / Num. unique obs: 2096 / CC1/2: 0.508 / Rrim(I) all: 0.985

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→45.14 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 1981 5.73 %
Rwork0.1875 --
obs0.189 34543 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 368 2924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082621
X-RAY DIFFRACTIONf_angle_d1.1243573
X-RAY DIFFRACTIONf_dihedral_angle_d6.495344
X-RAY DIFFRACTIONf_chiral_restr0.07423
X-RAY DIFFRACTIONf_plane_restr0.008449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.3819690.36021305X-RAY DIFFRACTION53
1.82-1.870.34541190.30521786X-RAY DIFFRACTION72
1.87-1.930.27821270.25162068X-RAY DIFFRACTION83
1.93-1.990.28021180.23512198X-RAY DIFFRACTION89
1.99-2.060.2951540.21922348X-RAY DIFFRACTION94
2.06-2.150.21041500.18682451X-RAY DIFFRACTION99
2.15-2.240.19691540.18892489X-RAY DIFFRACTION100
2.24-2.360.23171540.1922516X-RAY DIFFRACTION100
2.36-2.510.21661500.18742514X-RAY DIFFRACTION100
2.51-2.70.22741520.20372508X-RAY DIFFRACTION100
2.7-2.970.21771540.19382537X-RAY DIFFRACTION100
2.97-3.410.22331620.18852548X-RAY DIFFRACTION100
3.41-4.290.20251510.15932590X-RAY DIFFRACTION100
4.29-45.140.15111670.15842704X-RAY DIFFRACTION100

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