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- PDB-8jj9: Human FAM91A1 N terminal domain in complex with TBC1D23 -

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Basic information

Entry
Database: PDB / ID: 8jj9
TitleHuman FAM91A1 N terminal domain in complex with TBC1D23
Components
  • Protein FAM91A1
  • TBC1 domain family member 23
KeywordsTRANSPORT PROTEIN/UNKNOWN FUNCTION / TRANSPORT PROTEIN-UNKNOWN FUNCTION complex
Function / homology
Function and homology information


vesicle tethering to Golgi / embryonic brain development / retrograde transport, endosome to Golgi / RHOH GTPase cycle / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / brain development / neuron projection development / cytoplasmic vesicle ...vesicle tethering to Golgi / embryonic brain development / retrograde transport, endosome to Golgi / RHOH GTPase cycle / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / brain development / neuron projection development / cytoplasmic vesicle / Golgi apparatus / cytosol
Similarity search - Function
FAM91, N-terminal domain / FAM91, C-terminal domain / FAM91 / FAM91 N-terminus / FAM91 C-terminus / TBC1 domain family member 23 / TBC1 domain family member 23, C-terminal domain / TBC1 domain family member 23 C-terminal / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain ...FAM91, N-terminal domain / FAM91, C-terminal domain / FAM91 / FAM91 N-terminus / FAM91 C-terminus / TBC1 domain family member 23 / TBC1 domain family member 23, C-terminal domain / TBC1 domain family member 23 C-terminal / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
Protein FAM91A1 / TBC1 domain family member 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsDeng, H.Q. / Zhang, S.T. / Jia, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92254302 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: FAM91A1-TBC1D23 complex structure reveals human genetic variations susceptible for PCH.
Authors: Zhao, L. / Deng, H. / Yang, Q. / Tang, Y. / Zhao, J. / Li, P. / Zhang, S. / Yong, X. / Li, T. / Billadeau, D.D. / Jia, D.
History
DepositionMay 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FAM91A1
B: Protein FAM91A1
C: TBC1 domain family member 23
D: TBC1 domain family member 23


Theoretical massNumber of molelcules
Total (without water)77,5834
Polymers77,5834
Non-polymers00
Water3,045169
1
A: Protein FAM91A1
B: Protein FAM91A1
C: TBC1 domain family member 23
D: TBC1 domain family member 23

A: Protein FAM91A1
B: Protein FAM91A1
C: TBC1 domain family member 23
D: TBC1 domain family member 23

A: Protein FAM91A1
B: Protein FAM91A1
C: TBC1 domain family member 23
D: TBC1 domain family member 23


Theoretical massNumber of molelcules
Total (without water)232,74912
Polymers232,74912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
Buried area2000 Å2
ΔGint-12 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.212, 93.558, 111.514
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 Protein FAM91A1


Mass: 36426.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM91A1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q658Y4
#2: Protein/peptide TBC1 domain family member 23 / HCV non-structural protein 4A-transactivated protein 1


Mass: 2364.706 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D23
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9NUY8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tetraethylene glycol, Pentaethylene glycol, PH8.5 Tris, Ethylene glycol, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.51→111.51 Å / Num. obs: 32278 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 11.6
Reflection shellResolution: 2.51→2.58 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2358 / Rpim(I) all: 0.885 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
DIALSdata scaling
PDB_EXTRACTdata extraction
autoPROCdata reduction
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→41.01 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.67 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 1592 4.95 %
Rwork0.2245 --
obs0.2252 32210 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5229 0 0 169 5398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115346
X-RAY DIFFRACTIONf_angle_d1.1367228
X-RAY DIFFRACTIONf_dihedral_angle_d6.83713
X-RAY DIFFRACTIONf_chiral_restr0.056791
X-RAY DIFFRACTIONf_plane_restr0.012917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.590.35771640.29172734X-RAY DIFFRACTION100
2.59-2.680.35881520.2772716X-RAY DIFFRACTION100
2.68-2.790.29911350.26262755X-RAY DIFFRACTION100
2.79-2.920.30321500.24922723X-RAY DIFFRACTION100
2.92-3.070.29581270.22822767X-RAY DIFFRACTION100
3.07-3.260.25371440.23022771X-RAY DIFFRACTION100
3.26-3.520.2861160.22352782X-RAY DIFFRACTION100
3.52-3.870.26291530.19872767X-RAY DIFFRACTION100
3.87-4.430.22861450.18082814X-RAY DIFFRACTION100
4.43-5.580.22271340.19482837X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 38.4602 Å / Origin y: 0.2825 Å / Origin z: 28.4806 Å
111213212223313233
T0.0681 Å2-0.0157 Å20.0148 Å2-0.0679 Å2-0.048 Å2--0.0318 Å2
L0.4535 °2-0.169 °20.0506 °2-0.303 °2-0.0354 °2--0.1273 °2
S-0.0441 Å °0.0739 Å °-0.0196 Å °-0.0155 Å °-0.0325 Å °0.0227 Å °-0.0268 Å °-0.0427 Å °-0.1346 Å °
Refinement TLS groupSelection details: all

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