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- PDB-6jm5: Crystal structure of TBC1D23 C terminal domain -

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Basic information

Entry
Database: PDB / ID: 6jm5
TitleCrystal structure of TBC1D23 C terminal domain
ComponentsTBC1 domain family member 23
KeywordsPROTEIN TRANSPORT / membrane fusion / bridging factor / endosomal tranport
Function / homology
Function and homology information


vesicle tethering to Golgi / embryonic brain development / retrograde transport, endosome to Golgi / vesicle-mediated transport / brain development / trans-Golgi network / neuron projection development / cytoplasmic vesicle / Golgi apparatus / cytosol
Similarity search - Function
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. ...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
TBC1 domain family member 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSun, Q. / Huang, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural and functional studies of TBC1D23 C-terminal domain provide a link between endosomal trafficking and PCH.
Authors: Huang, W. / Liu, Z. / Yang, F. / Zhou, H. / Yong, X. / Yang, X. / Zhou, Y. / Xue, L. / Zhang, Y. / Liu, D. / Meng, W. / Zhang, W. / Zhang, X. / Shen, X. / Sun, Q. / Li, L. / Ma, C. / Wei, Y. ...Authors: Huang, W. / Liu, Z. / Yang, F. / Zhou, H. / Yong, X. / Yang, X. / Zhou, Y. / Xue, L. / Zhang, Y. / Liu, D. / Meng, W. / Zhang, W. / Zhang, X. / Shen, X. / Sun, Q. / Li, L. / Ma, C. / Wei, Y. / Billadeau, D.D. / Mo, X. / Jia, D.
History
DepositionMar 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2019Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct.title
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TBC1 domain family member 23
B: TBC1 domain family member 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8113
Polymers27,7882
Non-polymers231
Water4,558253
1
A: TBC1 domain family member 23


Theoretical massNumber of molelcules
Total (without water)13,8941
Polymers13,8941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TBC1 domain family member 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9172
Polymers13,8941
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.822, 48.950, 47.439
Angle α, β, γ (deg.)90.000, 109.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

21A-237-

HOH

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Components

#1: Protein TBC1 domain family member 23 / HCV non-structural protein 4A-transactivated protein 1


Mass: 13894.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D23, NS4ATP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NUY8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MES pH6.5, 0.5 M Ammonium nitrate, 25% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 37552 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Rrim(I) all: 0.061 / Χ2: 0.889 / Net I/σ(I): 7.4 / Num. measured all: 251366
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.6-1.636.718860.6580.6410.74399.7
1.63-1.666.718510.7560.5210.77100
1.66-1.696.718670.7790.4180.77100
1.69-1.726.718630.8540.3370.78699.90.8170.885
1.72-1.766.718970.8850.2630.81399.80.6320.686
1.76-1.86.418300.9150.2220.82599.90.5250.571
1.8-1.856.218960.9410.170.92699.50.3940.43
1.85-1.96.918840.9610.1310.9711000.3210.347
1.9-1.956.918570.9770.0980.97599.80.240.259
1.95-2.026.818810.9820.0751.0399.60.1820.197
2.02-2.096.718590.9850.0651.07599.70.1550.169
2.09-2.176.418600.9870.0541.09699.40.1270.138
2.17-2.276.518880.990.0441.12899.70.1050.114
2.27-2.39718700.9930.0371.07599.70.090.098
2.39-2.546.918970.9930.0311.00299.60.0770.083
2.54-2.746.718900.9940.0270.96699.60.0650.07
2.74-3.016.618600.9960.0220.87198.90.0520.057
3.01-3.45718950.9970.0180.75899.70.0430.047
3.45-4.346.518870.9980.0160.65598.80.0370.041
4.34-506.819340.9950.0150.5598.30.0350.038

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→45.53 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.245 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1614 4.6 %RANDOM
Rwork0.1567 ---
obs0.159 33125 91.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.25 Å2 / Biso mean: 20.323 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0.68 Å2
2---1.12 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: final / Resolution: 1.6→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 1 253 2188
Biso mean--30 33.23 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0142002
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171920
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.6512702
X-RAY DIFFRACTIONr_angle_other_deg0.8951.644502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27722.94185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50915388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.387158
X-RAY DIFFRACTIONr_chiral_restr0.0610.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_rigid_bond_restr6.30233922
X-RAY DIFFRACTIONr_sphericity_free33.7485155
X-RAY DIFFRACTIONr_sphericity_bonded23.78153994
LS refinement shellResolution: 1.595→1.637 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 45 -
Rwork0.223 1078 -
all-1123 -
obs--40.16 %

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