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- PDB-2pm6: Crystal Structure of yeast Sec13/31 edge element of the COPII ves... -

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Basic information

Entry
Database: PDB / ID: 2pm6
TitleCrystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native version
Components
  • Protein transport protein SEC13Protein targeting
  • Protein transport protein SEC31Protein targeting
KeywordsPROTEIN TRANSPORT / beta propeller / alpha solenoid
Function / homology
Function and homology information


Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / COPII vesicle coat ...Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / mating projection tip / endoplasmic reticulum organization / nucleocytoplasmic transport / vacuolar membrane / positive regulation of TOR signaling / mRNA transport / endoplasmic reticulum exit site / nuclear pore / : / positive regulation of TORC1 signaling / cell periphery / intracellular protein transport / protein import into nucleus / nuclear envelope / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1030 / Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 / Sec13/Seh1 family / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1030 / Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 / Sec13/Seh1 family / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein transport protein SEC31 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsGoldberg, J. / Fath, S. / Mancias, J.D. / Bi, X.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structure and Organization of Coat Proteins in the COPII Cage.
Authors: Fath, S. / Mancias, J.D. / Bi, X. / Goldberg, J.
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein transport protein SEC31
B: Protein transport protein SEC13
C: Protein transport protein SEC31
D: Protein transport protein SEC13


Theoretical massNumber of molelcules
Total (without water)155,3014
Polymers155,3014
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-113 kcal/mol
Surface area57700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.387, 52.343, 133.128
Angle α, β, γ (deg.)90.000, 108.620, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly unit involves this structure of the Sec13/31 edge element together with the Sec13/31 vertex element.

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Components

#1: Protein Protein transport protein SEC31 / Protein targeting / Protein WEB1


Mass: 44567.465 Da / Num. of mol.: 2 / Fragment: residues 370-763
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: WEB1, SEC31 / Production host: Hi5 insect cells / References: UniProt: P38968
#2: Protein Protein transport protein SEC13 / Protein targeting


Mass: 33082.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC13, ANU3 / Production host: Hi5 insect cells / References: UniProt: Q04491
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 4000, 10% DMSO, 6% dioxanie, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2006 / Details: multi-layer
RadiationMonochromator: multi-layer device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 59486 / Num. obs: 56172 / % possible obs: 94.7 % / Observed criterion σ(F): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.041 / Rsym value: 0.04 / Net I/σ(I): 20
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.37 / Num. unique all: 5778 / Rsym value: 0.32 / % possible all: 93.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: From SAD/MAD-determined structure

Resolution: 2.45→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 2782 4.5 %random
Rwork0.251 ---
all0.254 59486 --
obs0.254 54986 88 %-
Solvent computationBsol: 40.186 Å2
Displacement parametersBiso mean: 68.727 Å2
Baniso -1Baniso -2Baniso -3
1-16.723 Å20 Å2-6.464 Å2
2---29.362 Å20 Å2
3---12.639 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9934 0 0 261 10195
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.319
X-RAY DIFFRACTIONc_mcbond_it3.7153.5
X-RAY DIFFRACTIONc_scbond_it4.5724
X-RAY DIFFRACTIONc_mcangle_it5.5684
X-RAY DIFFRACTIONc_scangle_it6.2654.5
LS refinement shellResolution: 2.45→2.47 Å /
RfactorNum. reflection
Rfree0.536 46
Rwork0.498 -
obs-906
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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