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- PDB-5azx: Crystal structure of p24delta1 GOLD domain (native 1) -

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Basic information

Entry
Database: PDB / ID: 5azx
TitleCrystal structure of p24delta1 GOLD domain (native 1)
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 / SAD / Resolution: 1.58 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 10
B: Transmembrane emp24 domain-containing protein 10
C: Transmembrane emp24 domain-containing protein 10
D: Transmembrane emp24 domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8649
Polymers45,3834
Non-polymers4805
Water1,62190
1
A: Transmembrane emp24 domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4422
Polymers11,3461
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transmembrane emp24 domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5383
Polymers11,3461
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
4
D: Transmembrane emp24 domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5383
Polymers11,3461
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.232, 74.392, 79.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4 / Fragment: UNP residues 32-132 / Mutation: L1G/G2S
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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate (pH 5.5) and 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.58→100 Å / Num. obs: 56232 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rsym value: 0.057 / Net I/σ(I): 78.7
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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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: 1.58→33.72 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 2841 5.07 %Random selection
Rwork0.2296 ---
obs0.2306 56063 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→33.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 25 90 3131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073098
X-RAY DIFFRACTIONf_angle_d0.8624162
X-RAY DIFFRACTIONf_dihedral_angle_d11.9381830
X-RAY DIFFRACTIONf_chiral_restr0.061460
X-RAY DIFFRACTIONf_plane_restr0.004527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60720.2841040.24622668X-RAY DIFFRACTION100
1.6072-1.63650.2851450.24862628X-RAY DIFFRACTION100
1.6365-1.66790.26871500.24392652X-RAY DIFFRACTION100
1.6679-1.7020.31081550.23522637X-RAY DIFFRACTION100
1.702-1.7390.2411340.23992634X-RAY DIFFRACTION100
1.739-1.77940.25731410.23952639X-RAY DIFFRACTION100
1.7794-1.82390.311330.24022647X-RAY DIFFRACTION100
1.8239-1.87320.27661570.23972647X-RAY DIFFRACTION100
1.8732-1.92840.24981330.22662627X-RAY DIFFRACTION100
1.9284-1.99060.23911560.23012669X-RAY DIFFRACTION100
1.9906-2.06170.23381380.22532678X-RAY DIFFRACTION100
2.0617-2.14430.24611490.22492662X-RAY DIFFRACTION100
2.1443-2.24180.27821360.22812647X-RAY DIFFRACTION100
2.2418-2.360.26661660.24052660X-RAY DIFFRACTION100
2.36-2.50780.27671520.24382659X-RAY DIFFRACTION100
2.5078-2.70140.26121370.24752688X-RAY DIFFRACTION100
2.7014-2.97310.30691240.24882748X-RAY DIFFRACTION100
2.9731-3.40290.23151270.22782719X-RAY DIFFRACTION100
3.4029-4.2860.20451580.2012691X-RAY DIFFRACTION99
4.286-33.7280.23151460.22542622X-RAY DIFFRACTION91

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