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- PDB-5h3j: Crystal structure of Grasp domain of Grasp55 complexed with the G... -

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Basic information

Entry
Database: PDB / ID: 5h3j
TitleCrystal structure of Grasp domain of Grasp55 complexed with the Golgin45 C-terminus
Components
  • Golgi reassembly-stacking protein 2
  • Golgin-45BLZF1
KeywordsPROTEIN TRANSPORT / PDZ DOMAIN / GOLGI peripheral membrane PROTEIN / GOLGIN / TETHERING PROTEIN
Function / homology
Function and homology information


Golgi Cisternae Pericentriolar Stack Reorganization / establishment of protein localization to plasma membrane / organelle assembly / organelle organization / Golgi to plasma membrane protein transport / Golgi medial cisterna / Golgi organization / response to endoplasmic reticulum stress / spermatogenesis / cell differentiation ...Golgi Cisternae Pericentriolar Stack Reorganization / establishment of protein localization to plasma membrane / organelle assembly / organelle organization / Golgi to plasma membrane protein transport / Golgi medial cisterna / Golgi organization / response to endoplasmic reticulum stress / spermatogenesis / cell differentiation / Golgi membrane / ubiquitin protein ligase binding / endoplasmic reticulum membrane / Golgi apparatus / enzyme binding / nucleoplasm / nucleus
Similarity search - Function
Golgin-45 / DASH complex subunit Hsk3-like / DASH complex subunit Hsk3 like / GRASP55/65 / GRASP-type PDZ domain / GRASP55/65 PDZ-like domain / GRASP-type PDZ domain profile. / PDZ domain / Pdz3 Domain / PDZ superfamily ...Golgin-45 / DASH complex subunit Hsk3-like / DASH complex subunit Hsk3 like / GRASP55/65 / GRASP-type PDZ domain / GRASP55/65 PDZ-like domain / GRASP-type PDZ domain profile. / PDZ domain / Pdz3 Domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Golgin-45 / Golgi reassembly-stacking protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsShi, N. / Zhao, J. / Li, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370738 China
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Basis for the Interaction between Golgi Reassembly-stacking Protein GRASP55 and Golgin45
Authors: Zhao, J. / Li, B. / Huang, X. / Morelli, X. / Shi, N.
History
DepositionOct 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Golgi reassembly-stacking protein 2
B: Golgin-45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3693
Polymers26,3032
Non-polymers651
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-56 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.681, 35.855, 64.030
Angle α, β, γ (deg.)90.00, 93.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-655-

HOH

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Components

#1: Protein Golgi reassembly-stacking protein 2 / GRASP55 / GRS2 / Golgi reassembly-stacking protein of 55 kDa


Mass: 23029.691 Da / Num. of mol.: 1 / Fragment: Grasp domain, UNP residues 2-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gorasp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99JX3
#2: Protein/peptide Golgin-45 / BLZF1 / Basic leucine zipper nuclear factor 1


Mass: 3273.655 Da / Num. of mol.: 1 / Fragment: UNP residues 379-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Blzf1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R2X8
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 1.97 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG4000, potassium sodium tartrate, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97368 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97368 Å / Relative weight: 1
ReflectionResolution: 1.25→33.65 Å / Num. obs: 122914 / % possible obs: 99.81 % / Redundancy: 7.2 % / Net I/σ(I): 8.38
Reflection shellResolution: 1.25→1.295 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RLE

3rle


Resolution: 1.33→31.954 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1623 3899 3.92 %
Rwork0.1369 --
obs0.1379 99439 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→31.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 1 386 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091757
X-RAY DIFFRACTIONf_angle_d1.2352396
X-RAY DIFFRACTIONf_dihedral_angle_d12.019647
X-RAY DIFFRACTIONf_chiral_restr0.074266
X-RAY DIFFRACTIONf_plane_restr0.006317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.34620.25211550.24863280X-RAY DIFFRACTION98
1.3462-1.36330.25651440.21613404X-RAY DIFFRACTION100
1.3633-1.38120.18731120.20073485X-RAY DIFFRACTION100
1.3812-1.40010.22551360.18833394X-RAY DIFFRACTION100
1.4001-1.42010.21541240.17563423X-RAY DIFFRACTION100
1.4201-1.44130.20391590.17713429X-RAY DIFFRACTION100
1.4413-1.46380.19871060.16813372X-RAY DIFFRACTION100
1.4638-1.48780.20761590.15643482X-RAY DIFFRACTION100
1.4878-1.51350.18651420.15033330X-RAY DIFFRACTION100
1.5135-1.5410.18331480.14593437X-RAY DIFFRACTION100
1.541-1.57070.17861440.13323452X-RAY DIFFRACTION100
1.5707-1.60270.1611330.13073399X-RAY DIFFRACTION100
1.6027-1.63760.15351480.12943422X-RAY DIFFRACTION100
1.6376-1.67570.14621450.12393383X-RAY DIFFRACTION100
1.6757-1.71760.16791280.12643446X-RAY DIFFRACTION100
1.7176-1.7640.18091290.12313398X-RAY DIFFRACTION100
1.764-1.81590.16471530.13183427X-RAY DIFFRACTION100
1.8159-1.87450.18781360.12883418X-RAY DIFFRACTION100
1.8745-1.94150.17651450.12563389X-RAY DIFFRACTION100
1.9415-2.01920.1461390.12293449X-RAY DIFFRACTION100
2.0192-2.11110.14261360.11583417X-RAY DIFFRACTION100
2.1111-2.22240.16861500.12413417X-RAY DIFFRACTION100
2.2224-2.36160.15111400.12663433X-RAY DIFFRACTION100
2.3616-2.54380.15861460.13333366X-RAY DIFFRACTION100
2.5438-2.79970.15991350.1433421X-RAY DIFFRACTION100
2.7997-3.20450.16011340.13963441X-RAY DIFFRACTION100
3.2045-4.03610.13621440.1233416X-RAY DIFFRACTION100
4.0361-31.96310.15131290.14453410X-RAY DIFFRACTION100

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