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- PDB-5azy: Crystal structure of p24delta1 GOLD domain (Native 2) -

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Basic information

Entry
Database: PDB / ID: 5azy
TitleCrystal structure of p24delta1 GOLD domain (Native 2)
ComponentsTransmembrane emp24 domain-containing protein 10
KeywordsPROTEIN TRANSPORT / GPI-anchored protein / p24 complex
Function / homology
Function and homology information


vesicle targeting, to, from or within Golgi / COPI-coated vesicle budding / protein localization to ERGIC / cytosol to ERGIC protein transport / regulation of amyloid-beta formation / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / vesicle targeting / COPI-coated vesicle ...vesicle targeting, to, from or within Golgi / COPI-coated vesicle budding / protein localization to ERGIC / cytosol to ERGIC protein transport / regulation of amyloid-beta formation / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / vesicle targeting / COPI-coated vesicle / Cargo concentration in the ER / gamma-secretase complex / COPII-mediated vesicle transport / zymogen granule membrane / regulated exocytosis / positive regulation of interleukin-1 production / trans-Golgi network transport vesicle / cis-Golgi network / response to alkaloid / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / syntaxin binding / transport vesicle membrane / COPII-coated ER to Golgi transport vesicle / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / protein transmembrane transporter activity / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / kidney development / positive regulation of protein secretion / intracellular protein transport / melanosome / Golgi membrane / protein-containing complex binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
emp24/gp25L/p24 family/GOLD / emp24/gp25L/p24 family/GOLD / Transmembrane emp24 domain-containing protein / GOLD domain / GOLD domain profile.
Similarity search - Domain/homology
Transmembrane emp24 domain-containing protein 10
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Revision 1.3Nov 8, 2023Group: 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: Transmembrane emp24 domain-containing protein 10
B: Transmembrane emp24 domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9465
Polymers22,6922
Non-polymers2543
Water55831
1
A: Transmembrane emp24 domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6004
Polymers11,3461
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transmembrane emp24 domain-containing protein 10


Theoretical massNumber of molelcules
Total (without water)11,3461
Polymers11,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-26 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.798, 77.354, 41.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transmembrane emp24 domain-containing protein 10 / 21 kDa transmembrane-trafficking protein / Transmembrane protein Tmp21 / p24 family protein delta-1 ...21 kDa transmembrane-trafficking protein / Transmembrane protein Tmp21 / p24 family protein delta-1 / p24delta1


Mass: 11345.822 Da / Num. of mol.: 2 / Fragment: UNP residues 32-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Tmed10, Tmp21 / Plasmid: pCOLD / Production host: Escherichia coli (E. coli) / References: UniProt: Q63584
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium citrate (pH 7.0)

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 20574 / % possible obs: 98 % / Redundancy: 7.1 % / Rsym value: 0.067 / Net I/σ(I): 56.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AZX

5azx


Resolution: 1.8→33.471 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2805 1044 5.16 %Random selection
Rwork0.2329 ---
obs0.2354 20217 97.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→33.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 14 31 1544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061545
X-RAY DIFFRACTIONf_angle_d0.8752072
X-RAY DIFFRACTIONf_dihedral_angle_d13.714917
X-RAY DIFFRACTIONf_chiral_restr0.061231
X-RAY DIFFRACTIONf_plane_restr0.004262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.89490.2781450.24612740X-RAY DIFFRACTION100
1.8949-2.01360.29021430.22492736X-RAY DIFFRACTION100
2.0136-2.16910.2951620.2192744X-RAY DIFFRACTION100
2.1691-2.38730.25011420.23492785X-RAY DIFFRACTION100
2.3873-2.73260.29671510.24872781X-RAY DIFFRACTION100
2.7326-3.44230.29461590.23872831X-RAY DIFFRACTION100
3.4423-33.47690.26961420.22592556X-RAY DIFFRACTION87

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