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- PDB-2zmv: Crystal structure of Synbindin -

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Basic information

Entry
Database: PDB / ID: 2zmv
TitleCrystal structure of Synbindin
ComponentsTrafficking protein particle complex subunit 4
KeywordsTRANSPORT PROTEIN / longin domain / Synbindin / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Transport
Function / homology
Function and homology information


vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / Golgi stack / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / Syndecan interactions ...vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / Golgi stack / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / Syndecan interactions / dendrite development / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagy / synaptic vesicle / postsynaptic membrane / Golgi membrane / dendrite / synapse / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Beta-Lactamase - #70 / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Trafficking protein particle complex subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsFan, F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structure of human synbindin reveals two conformations of longin domain
Authors: Fan, S. / Wei, Z. / Xu, H. / Gong, W.
History
DepositionApr 21, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trafficking protein particle complex subunit 4
B: Trafficking protein particle complex subunit 4


Theoretical massNumber of molelcules
Total (without water)50,8742
Polymers50,8742
Non-polymers00
Water0
1
A: Trafficking protein particle complex subunit 4
B: Trafficking protein particle complex subunit 4

A: Trafficking protein particle complex subunit 4
B: Trafficking protein particle complex subunit 4

A: Trafficking protein particle complex subunit 4
B: Trafficking protein particle complex subunit 4


Theoretical massNumber of molelcules
Total (without water)152,6236
Polymers152,6236
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area12650 Å2
ΔGint-80 kcal/mol
Surface area59960 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-10 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.391, 124.391, 124.391
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Trafficking protein particle complex subunit 4 / Synbindin / TRS23 homolog / Hematopoietic stem/progenitor cell protein 172


Mass: 25437.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAPPC4, SBDN, CGI-104, HSPC172, PTD009 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9Y296

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% MPD, 3% EG, 1% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONBSRF 3W1A10.9787, 0.9500, 0.9793
ROTATING ANODERIGAKU FR-E+ DW21.5418
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDFeb 19, 2005
RIGAKU RAXIS IV++2IMAGE PLATEApr 11, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITEMADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.951
30.97931
41.54181
ReflectionResolution: 2.8→50 Å / Num. obs: 16132 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 91.3 Å2 / Rmerge(I) obs: 0.044

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 2.8→30.17 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.888 / SU B: 31.559 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.662 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28962 792 5.1 %RANDOM
Rwork0.2427 ---
obs0.24512 14891 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 73.717 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 0 0 3205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.984030
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9535394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48323.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91315440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9771511
X-RAY DIFFRACTIONr_chiral_restr0.070.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022221
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21168
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21996
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.60422034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.32233097
X-RAY DIFFRACTIONr_scbond_it2.25531061
X-RAY DIFFRACTIONr_scangle_it3.1054933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 55 -
Rwork0.338 1127 -
obs--99.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.340.6641-1.42491.81370.06092.40360.1433-0.2909-0.063-0.1-0.0425-0.21760.04050.0809-0.10080.0767-0.0547-0.0077-0.01470.0319-0.026250.29238.347318.6709
21.73072.0959-5.04563.3296-4.731817.1101-0.38480.1801-0.5744-0.70320.3667-1.05550.8734-1.20240.01820.22040.14260.3251-0.007-0.26280.239170.233640.5235-2.8951
317.36815.64061.746814.88638.00127.7574-0.6772-0.9906-1.47241.90420.394-1.78590.95541.57390.28320.46010.44520.16270.07890.01760.439479.007138.99382.0479
40.84880.4669-0.72154.8312-0.42791.66660.0546-0.05880.09-0.53920.06310.13750.1828-0.1837-0.1177-0.0004-0.03390.0109-0.00750.0227-0.065746.296539.044412.3206
50.71041.4552-0.53516.0482-0.026113.05470.4495-0.1779-0.18480.2768-0.3235-0.52950.2673-0.5554-0.126-0.0022-0.03830.0275-0.04840.1186-0.039749.533928.911522.59
611.8063.2074-0.053512.7155-4.70711.85940.2714-1.6282-0.05580.753-1.1599-0.8433-0.3651-0.09560.88860.0996-0.1536-0.04330.08970.0733-0.046366.123158.722127.7156
74.33752.9627-0.743522.13540.11047.55040.3403-0.4785-1.02990.4115-0.3168-1.47440.5420.5575-0.02350.14850.0375-0.1707-0.1324-0.02860.071477.718972.580345.3521
814.0203-1.3495-4.169335.6497-2.502419.206-0.5827-1.1429-0.7455.54791.08451.10382.38040.0196-0.50180.8688-0.1307-0.0524-0.36190.2643-0.20972.544269.421154.1657
95.1984.5990.59654.38750.03250.8386-0.21350.1383-0.29420.0682-0.0233-0.359-0.1471-0.0730.2368-0.0591-0.037-0.0246-0.09280.02590.124868.573259.080819.957
1022.10525.91191.88482.2909-0.65542.05470.6074-1.9224-1.73370.6814-0.4798-0.4908-0.1508-0.3478-0.12770.0427-0.1719-0.0753-0.04660.1605-0.015161.784349.500225.8816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 19
2X-RAY DIFFRACTION2A20 - 61
3X-RAY DIFFRACTION3A62 - 100
4X-RAY DIFFRACTION4A101 - 183
5X-RAY DIFFRACTION5A184 - 213
6X-RAY DIFFRACTION6B2 - 24
7X-RAY DIFFRACTION7B25 - 67
8X-RAY DIFFRACTION8B68 - 99
9X-RAY DIFFRACTION9B100 - 186
10X-RAY DIFFRACTION10B187 - 211

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