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- PDB-8ybc: Crystal structure of coiled coil domain of Golm1 (Golgi membrane ... -

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Basic information

Entry
Database: PDB / ID: 8ybc
TitleCrystal structure of coiled coil domain of Golm1 (Golgi membrane protein 1)
ComponentsGolgi membrane protein 1
KeywordsONCOPROTEIN / tetramer / coiled coil / Alpha-Helix
Function / homology
Function and homology information


nucleus organization / regulation of lipid metabolic process / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / Golgi apparatus / extracellular space / plasma membrane
Similarity search - Function
Golgi membrane protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsXie, X. / Bai, W.F. / Shi, N.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: The first structure of human Golm1 coiled coil domain reveals an unexpected tetramer and highlights its structural diversity.
Authors: Bai, W. / Li, B. / Wu, P. / Li, X. / Huang, X. / Shi, N. / Yang, C. / Hu, F. / Xie, X.
History
DepositionFeb 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Golgi membrane protein 1
B: Golgi membrane protein 1
C: Golgi membrane protein 1
D: Golgi membrane protein 1


Theoretical massNumber of molelcules
Total (without water)32,5734
Polymers32,5734
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-96 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.810, 44.020, 63.800
Angle α, β, γ (deg.)90.000, 112.920, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Golgi membrane protein 1 / Golgi membrane protein GP73 / Golgi phosphoprotein 2


Mass: 8143.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOLM1, C9orf155, GOLPH2, PSEC0242, UNQ686/PRO1326 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta / References: UniProt: Q8NBJ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 5% PEG6000 / PH range: 6.0-6.5 / Temp details: 16 degrees centigrade

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.28→35.23 Å / Num. obs: 23659 / % possible obs: 90.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.79 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.126 / Net I/σ(I): 8
Reflection shellResolution: 2.28→2.34 Å / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12613 / CC1/2: 0.759 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→35.23 Å / SU ML: 0.356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.321 2387 10.09 %
Rwork0.2422 21272 -
obs0.25 23659 88.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.32 Å2
Refinement stepCycle: LAST / Resolution: 2.28→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 0 54 2204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822162
X-RAY DIFFRACTIONf_angle_d0.87762882
X-RAY DIFFRACTIONf_chiral_restr0.0395313
X-RAY DIFFRACTIONf_plane_restr0.0046387
X-RAY DIFFRACTIONf_dihedral_angle_d19.2547280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.330.43911370.34821252X-RAY DIFFRACTION88.64
2.33-2.380.3531550.28031415X-RAY DIFFRACTION99.18
2.38-2.430.31351590.25931408X-RAY DIFFRACTION99.05
2.43-2.490.32321680.26821388X-RAY DIFFRACTION99.42
2.49-2.560.35361540.26171414X-RAY DIFFRACTION98.68
2.56-2.640.35521620.25471388X-RAY DIFFRACTION98.41
2.64-2.720.3666300.2733308X-RAY DIFFRACTION21.05
2.72-2.820.32721510.23791380X-RAY DIFFRACTION98.84
2.82-2.930.32991710.24181438X-RAY DIFFRACTION98.89
2.93-3.060.30851570.24121378X-RAY DIFFRACTION98.78
3.06-3.230.38281580.24871396X-RAY DIFFRACTION98.54
3.23-3.410.27491360.23171267X-RAY DIFFRACTION95.96
3.47-3.640.2733910.2045814X-RAY DIFFRACTION89.34
3.7-4.060.31151110.20841013X-RAY DIFFRACTION74.54
4.06-4.650.36011400.21081324X-RAY DIFFRACTION93.61
4.65-5.850.26631540.23411370X-RAY DIFFRACTION96.21
5.86-35.230.31031530.27321319X-RAY DIFFRACTION92.81

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