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- PDB-7twd: Structure of AAGAB C-terminal dimerization domain -

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Basic information

Entry
Database: PDB / ID: 7twd
TitleStructure of AAGAB C-terminal dimerization domain
ComponentsAlpha- and gamma-adaptin-binding protein p34
KeywordsCHAPERONE / protein binding / membrane trafficking / AP Complex
Function / homologyAlpha/gamma-adaptin-binding protein p34 / protein transport / nuclear speck / cytosol / cytoplasm / PHOSPHATE ION / Alpha- and gamma-adaptin-binding protein p34
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsTian, 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: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Oligomer-to-monomer transition underlies the chaperone function of AAGAB in AP1/AP2 assembly.
Authors: Tian, Y. / Datta, I. / Yang, R. / Wan, C. / Wang, B. / Crisman, L. / He, H. / Brautigam, C.A. / Li, S. / Shen, J. / Yin, Q.
History
DepositionFeb 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5584
Polymers10,3682
Non-polymers1902
Water1,33374
1
A: Alpha- and gamma-adaptin-binding protein p34
B: Alpha- and gamma-adaptin-binding protein p34
hetero molecules

A: Alpha- and gamma-adaptin-binding protein p34
B: Alpha- and gamma-adaptin-binding protein p34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1168
Polymers20,7364
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454y-1,-x+y,z-1/61
Unit cell
Length a, b, c (Å)47.539, 47.539, 191.394
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein/peptide Alpha- and gamma-adaptin-binding protein p34


Mass: 5184.021 Da / Num. of mol.: 2
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30% glycerol, 0.5 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9351 / % possible obs: 99.2 % / Redundancy: 13.5 % / Biso Wilson estimate: 22.72 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.057 / Rrim(I) all: 0.213 / Χ2: 0.458 / Net I/σ(I): 17.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 0.929 / Num. unique obs: 900 / CC1/2: 0.38 / CC star: 0.742 / Rpim(I) all: 0.479 / Rrim(I) all: 1.658 / Χ2: 0.458 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→40.25 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.4306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2598 801 10.01 %
Rwork0.2125 7198 -
obs0.2172 7999 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.63 Å2
Refinement stepCycle: LAST / Resolution: 2.11→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms723 0 10 74 807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017763
X-RAY DIFFRACTIONf_angle_d0.44391020
X-RAY DIFFRACTIONf_chiral_restr0.0287104
X-RAY DIFFRACTIONf_plane_restr0.0022129
X-RAY DIFFRACTIONf_dihedral_angle_d1.6418652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.240.29811300.25561169X-RAY DIFFRACTION99.92
2.24-2.420.31111290.22941171X-RAY DIFFRACTION100
2.42-2.660.28811320.20981182X-RAY DIFFRACTION99.92
2.66-3.040.27651320.21511187X-RAY DIFFRACTION100
3.04-3.830.21251350.1941212X-RAY DIFFRACTION99.19
3.83-40.250.25171430.20891277X-RAY DIFFRACTION94.86
Refinement TLS params.Method: refined / Origin x: -24.1235768997 Å / Origin y: 10.4592267274 Å / Origin z: -1.3874935756 Å
111213212223313233
T0.227619564393 Å2-0.0137761877942 Å2-0.0419396608322 Å2-0.050060053266 Å2-0.00269369905998 Å2--0.185332740203 Å2
L1.30739737523 °20.0763836534454 °20.696177313807 °2-0.735707003782 °20.101914878785 °2--1.80733159376 °2
S0.0257481378697 Å °0.0419038753117 Å °-0.636471458411 Å °0.0161397982192 Å °0.347407169419 Å °-0.0674086658862 Å °0.853628334205 Å °0.128562084714 Å °-0.140085524503 Å °
Refinement TLS groupSelection details: all

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