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- PDB-5azw: Crystal structure of p24beta1 GOLD domain -

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Basic information

Entry
Database: PDB / ID: 5azw
TitleCrystal structure of p24beta1 GOLD domain
ComponentsTransmembrane emp24 domain-containing protein 2
KeywordsPROTEIN TRANSPORT / GPI-anchored protein / p24 complex
Function / homology
Function and homology information


COPI coating of Golgi vesicle / endoplasmic reticulum membrane organization / COPI-coated vesicle membrane / regulation of SREBP signaling pathway / vesicle cargo loading / somite rostral/caudal axis specification / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / COPI-coated vesicle / maternal placenta development / zymogen granule membrane ...COPI coating of Golgi vesicle / endoplasmic reticulum membrane organization / COPI-coated vesicle membrane / regulation of SREBP signaling pathway / vesicle cargo loading / somite rostral/caudal axis specification / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / COPI-coated vesicle / maternal placenta development / zymogen granule membrane / PERK-mediated unfolded protein response / Pre-NOTCH Processing in Golgi / COPII vesicle coating / post-anal tail morphogenesis / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-mediated vesicle transport / negative regulation of GTPase activity / labyrinthine layer blood vessel development / COPI-dependent Golgi-to-ER retrograde traffic / Golgi cisterna membrane / heart looping / COPII-coated ER to Golgi transport vesicle / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / neural tube closure / protein localization to plasma membrane / intracellular protein transport / ER to Golgi transport vesicle membrane / multicellular organism growth / membrane => GO:0016020 / Golgi membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
emp24/gp25L/p24 family/GOLD / emp24/gp25L/p24 family/GOLD / Transmembrane emp24 domain-containing protein / GOLD domain superfamily / GOLD domain / GOLD domain profile.
Similarity search - Domain/homology
Transmembrane emp24 domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsNagae, M. / Yamaguchi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT25121738 Japan
CitationJournal: J.Mol.Biol. / Year: 2016
Title: 3D Structure and Interaction of p24 beta and p24 delta Golgi Dynamics Domains: Implication for p24 Complex Formation and Cargo Transport
Authors: Nagae, M. / Hirata, T. / Morita-Matsumoto, K. / Theiler, R. / Fujita, M. / Kinoshita, T. / Yamaguchi, Y.
History
DepositionOct 23, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane emp24 domain-containing protein 2
B: Transmembrane emp24 domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4644
Polymers21,3402
Non-polymers1242
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint2 kcal/mol
Surface area10090 Å2
Unit cell
Length a, b, c (Å)97.772, 35.664, 62.312
Angle α, β, γ (deg.)90.00, 129.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-312-

HOH

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Components

#1: Protein Transmembrane emp24 domain-containing protein 2 / Membrane protein p24A / p24 / p24 family protein beta-1 / p24beta1


Mass: 10670.019 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMED2, RNP24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15363
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 0.2 M sodium chloride and 25 % (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 31, 2012
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 26802 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rsym value: 0.046 / Net I/σ(I): 79
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 6.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→24.137 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1344 5.02 %Random selection
Rwork0.2208 ---
obs0.2214 26761 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→24.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 8 55 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071498
X-RAY DIFFRACTIONf_angle_d0.9692007
X-RAY DIFFRACTIONf_dihedral_angle_d9.464873
X-RAY DIFFRACTIONf_chiral_restr0.061212
X-RAY DIFFRACTIONf_plane_restr0.006257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.55360.29631290.24832552X-RAY DIFFRACTION99
1.5536-1.61580.29231260.23722530X-RAY DIFFRACTION100
1.6158-1.68930.23211220.22612540X-RAY DIFFRACTION100
1.6893-1.77840.23311310.23362521X-RAY DIFFRACTION100
1.7784-1.88970.2041360.22132558X-RAY DIFFRACTION100
1.8897-2.03560.22691270.21932534X-RAY DIFFRACTION100
2.0356-2.24030.26841310.22082574X-RAY DIFFRACTION100
2.2403-2.56420.24661410.24712543X-RAY DIFFRACTION100
2.5642-3.22940.24161550.22782570X-RAY DIFFRACTION100
3.2294-24.13970.20761460.19942495X-RAY DIFFRACTION95

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