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- PDB-5lz1: Crystal structure of human ACBD3 GOLD domain -

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Basic information

Entry
Database: PDB / ID: 5lz1
TitleCrystal structure of human ACBD3 GOLD domain
ComponentsGolgi resident protein GCP60
KeywordsSIGNALING PROTEIN / ACBD3 / GOLD
Function / homology
Function and homology information


fatty-acyl-CoA binding / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / Golgi membrane / Golgi apparatus / mitochondrion / membrane
Similarity search - Function
Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / FERM/acyl-CoA-binding protein superfamily
Similarity search - Domain/homology
Golgi resident protein GCP60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKlima, M. / Boura, E.
CitationJournal: Structure / Year: 2017
Title: Kobuviral Non-structural 3A Proteins Act as Molecular Harnesses to Hijack the Host ACBD3 Protein.
Authors: Klima, M. / Chalupska, D. / Rozycki, B. / Humpolickova, J. / Rezabkova, L. / Silhan, J. / Baumlova, A. / Dubankova, A. / Boura, E.
History
DepositionSep 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Golgi resident protein GCP60


Theoretical massNumber of molelcules
Total (without water)19,3891
Polymers19,3891
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.210, 56.210, 163.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Golgi resident protein GCP60 / Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi ...Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi phosphoprotein 1 / GOLPH1 / PBR- and PKA-associated protein 7 / Peripheral benzodiazepine receptor-associated protein PAP7


Mass: 19389.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACBD3, GCP60, GOCAP1, GOLPH1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9H3P7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100mM Tris pH 8.8, 25% w/v PEG 3.350, 20% glycerol, 20mM 2-propanol/1,2 -propanediol/1,3-propanediol/1-butanol/1,4-butanediol/1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.282724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282724 Å / Relative weight: 1
ReflectionResolution: 2→39.75 Å / Num. obs: 18582 / % possible obs: 99.85 % / Redundancy: 7.7 % / Biso Wilson estimate: 45.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05942 / Rsym value: 0.05942 / Net I/σ(I): 18.66
Reflection shellResolution: 2→2.071 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.349 / Mean I/σ(I) obs: 1.43 / CC1/2: 0.631 / % possible all: 99.45

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSversion Oct 15, 2015data reduction
XDSversion Oct 15, 2015data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OLM

1olm


Resolution: 2→39.746 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.66
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 930 5.01 %random selection
Rwork0.2181 ---
obs0.2195 18575 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 24 1172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031184
X-RAY DIFFRACTIONf_angle_d0.8961617
X-RAY DIFFRACTIONf_dihedral_angle_d12.549415
X-RAY DIFFRACTIONf_chiral_restr0.035171
X-RAY DIFFRACTIONf_plane_restr0.004206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10550.35661290.30172441X-RAY DIFFRACTION100
2.1055-2.23740.30041300.29182460X-RAY DIFFRACTION100
2.2374-2.41010.34171300.27032487X-RAY DIFFRACTION100
2.4101-2.65260.3161310.26452489X-RAY DIFFRACTION100
2.6526-3.03640.30861320.24692504X-RAY DIFFRACTION100
3.0364-3.8250.22741350.21182553X-RAY DIFFRACTION100
3.825-39.75430.20261430.18542711X-RAY DIFFRACTION100

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