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- PDB-2pm9: Crystal structure of yeast Sec13/31 vertex element of the COPII v... -

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Basic information

Entry
Database: PDB / ID: 2pm9
TitleCrystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat
Components
  • Protein transport protein SEC13
  • Protein transport protein SEC31
KeywordsPROTEIN TRANSPORT / beta propeller
Function / homology
Function and homology information


positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / COPII-mediated vesicle transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum ...positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / COPII-mediated vesicle transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coat / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / mating projection tip / SUMOylation of RNA binding proteins / endoplasmic reticulum organization / SUMOylation of chromatin organization proteins / vacuolar membrane / nucleocytoplasmic transport / endoplasmic reticulum exit site / positive regulation of TOR signaling / mRNA transport / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / nuclear envelope / protein transport / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum
Similarity search - Function
N-terminal domain of TfIIb - #400 / 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 / Sec16 Sec23-binding domain / Sec13/Seh1 family / N-terminal domain of TfIIb ...N-terminal domain of TfIIb - #400 / 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 / Sec16 Sec23-binding domain / Sec13/Seh1 family / N-terminal domain of TfIIb / Single Sheet / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Protein transport protein SEC31 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 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


Theoretical massNumber of molelcules
Total (without water)78,8422
Polymers78,8422
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-32 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.163, 155.163, 59.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
DetailsThe biological assembly unit involves this structure of the Sec13/31 vertex element together with the Sec13/31 edge element.

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Components

#1: Protein Protein transport protein SEC31 / Protein WEB1


Mass: 45651.285 Da / Num. of mol.: 1 / Fragment: residues 1-411
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


Mass: 33191.188 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 4.78 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 8% PEG 3350, 0.1M tri-sodium citrate, 10mM manganese chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. all: 21760 / Num. obs: 20444 / % possible obs: 92.6 % / Observed criterion σ(F): -5 / Observed criterion σ(I): -5 / Redundancy: 2.7 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.084 / Χ2: 2.081 / Net I/σ(I): 11.9
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1644 / Rsym value: 0.347 / Χ2: 1.289 / % possible all: 76.3

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Phasing

Phasing MRRfactor: 0.541 / Cor.coef. Fo:Fc: 0.202 / Cor.coef. Io to Ic: 0.219
Highest resolutionLowest resolution
Rotation3.5 Å8 Å
Translation3.5 Å8 Å
Phasing dmFOM : 0.48 / FOM acentric: 0.48 / FOM centric: 0.46 / Reflection: 18996 / Reflection acentric: 17786 / Reflection centric: 1210
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.4-37.9490.90.910.85884730154
5.9-9.40.710.720.627322474258
4.7-5.90.630.640.5234263188238
4.1-4.70.570.580.4834503256194
3.5-4.10.310.310.1957155442273
3.3-3.50.170.170.062789269693

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RESOLVE2.01phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: yeast Sec13

Resolution: 3.3→40 Å / FOM work R set: 0.753 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 959 4.4 %random
Rwork0.251 ---
all-21760 --
obs-18996 86.9 %-
Solvent computationBsol: 28.752 Å2
Displacement parametersBiso mean: 78.585 Å2
Baniso -1Baniso -2Baniso -3
1--10.926 Å20 Å20 Å2
2---10.926 Å20 Å2
3---21.851 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 0 28 5196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.636
X-RAY DIFFRACTIONc_mcbond_it4.0253.5
X-RAY DIFFRACTIONc_scbond_it3.9724
X-RAY DIFFRACTIONc_mcangle_it6.8424
X-RAY DIFFRACTIONc_scangle_it6.464.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.3-3.360.524350.404651686
3.36-3.420.45430.343708751
3.42-3.490.324540.323787841
3.49-3.570.412480.315848896
3.57-3.650.396520.355902954
3.65-3.740.442570.312931988
3.74-3.850.433490.2829791028
3.85-3.960.267460.23510081054
3.96-4.090.291520.2379761028
4.09-4.230.295520.23410111063
4.23-4.40.339400.2299971037
4.4-4.60.278640.2310321096
4.6-4.840.247450.20810311076
4.84-5.150.268570.2110361093
5.15-5.540.302520.21710301082
5.54-6.10.226430.18710311074
6.1-6.980.236530.20410191072
6.98-8.780.261560.22210321088
8.78-400.304610.30610281089
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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