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- PDB-2pm7: Crystal structure of yeast Sec13/31 edge element of the COPII ves... -

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Basic information

Entry
Database: PDB / ID: 2pm7
TitleCrystal structure of yeast Sec13/31 edge element of the COPII vesicular coat, selenomethionine 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 / vacuolar membrane / nucleocytoplasmic transport / 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 / SYNCHROTRON / SAD / Resolution: 2.35 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 / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)157,2924
Polymers157,2924
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-115 kcal/mol
Surface area57650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.190, 52.500, 133.090
Angle α, β, γ (deg.)90.00, 108.34, 90.00
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: 45126.602 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: 33519.457 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 4000, 10% DMSO, 6% dioxane, 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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2006
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 19.6 / Number: 232503 / Rmerge(I) obs: 0.047 / Χ2: 1.25 / D res high: 2.35 Å / D res low: 40 Å / Num. obs: 68569 / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.064087.710.0442.1293
4.025.069910.0391.7453.4
3.514.0299.710.0361.4183.5
3.193.5199.810.041.2483.5
2.963.1999.810.0571.1583.5
2.792.9699.910.0781.0713.5
2.652.7999.810.111.0213.5
2.532.659910.1490.973.4
2.432.5395.910.1960.9753.3
2.352.4391.110.2470.9543.2
ReflectionResolution: 2.35→40 Å / Num. all: 68569 / Num. obs: 68569 / % possible obs: 97.1 % / Observed criterion σ(F): -5 / Observed criterion σ(I): -5 / Redundancy: 3.4 % / Rmerge(I) obs: 0.047 / Χ2: 1.254 / Net I/σ(I): 19.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 4.55 / Num. unique all: 6339 / Rsym value: 0.247 / Χ2: 0.954 / % possible all: 91.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.6 Å / D res low: 38 Å / FOM : 0.31 / Reflection: 49627
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se21.0180.7640.5880.480.408
2Se14.3990.6780.1410.290.341
3Se29.0960.0360.1150.2260.393
4Se48.0220.5260.9520.2550.458
5Se34.3740.1790.1120.4450.399
6Se600.2720.2980.4630.532
7Se38.6970.5640.360.3670.332
8Se24.3860.770.3480.2140.286
9Se44.4030.7780.4220.4910.514
10Se49.1970.6920.0510.1290.365
11Se29.120.4470.2510.190.422
12Se56.6570.9790.3630.4450.536
13Se13.190.9670.4060.3940.171
14Se28.6380.3510.950.010.316
15Se39.5090.440.1990.190.423
16Se44.080.1170.1420.2720.317
17Se44.3760.5980.3780.3530.308
18Se44.9440.8040.1340.1050.241
19Se40.0990.8160.1570.0710.29
20Se44.350.0020.4170.4140.294
21Se45.1470.3660.2320.3740.406
22Se29.2170.6240.4910.2540.325
23Se59.7140.7430.6170.0910.486
24Se51.590.9720.3070.4440.474
25Se38.3880.1030.90.2050.269
26Se13.9280.1810.90.1010.164
27Se28.2650.3560.8980.0080.279
28Se35.8830.0340.2860.2190.259
Phasing MAD shell
Resolution (Å)FOM Reflection
9.31-380.251801
5.89-9.310.334215
4.61-5.890.355471
3.91-4.610.376441
3.46-3.910.367242
3.13-3.460.337871
2.88-3.130.288214
2.68-2.880.238372

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.35→30 Å / FOM work R set: 0.713 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 3487 4.9 %random
Rwork0.242 ---
all0.245 68569 --
obs0.245 68541 96.7 %-
Solvent computationBsol: 50.926 Å2
Displacement parametersBiso mean: 70.2 Å2
Baniso -1Baniso -2Baniso -3
1-19.799 Å20 Å2-3.493 Å2
2---35.418 Å20 Å2
3---15.62 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9934 0 0 261 10195
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.232
X-RAY DIFFRACTIONc_mcbond_it3.4873.5
X-RAY DIFFRACTIONc_scbond_it4.3594
X-RAY DIFFRACTIONc_mcangle_it5.0284
X-RAY DIFFRACTIONc_scangle_it5.8394.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.35-2.370.438640.45310411105
2.37-2.380.445720.4412271299
2.38-2.40.494580.43211891247
2.4-2.420.408710.4212211292
2.42-2.430.494510.40912441295
2.43-2.450.432660.40612341300
2.45-2.470.45550.37313021357
2.47-2.490.407690.36712741343
2.49-2.510.382790.35913311410
2.51-2.530.378690.32512061275
2.53-2.550.361780.33313171395
2.55-2.570.356710.30513081379
2.57-2.60.366510.3213531404
2.6-2.620.368810.33513591440
2.62-2.650.385620.33713071369
2.65-2.670.336670.3313241391
2.67-2.70.425670.29513231390
2.7-2.730.334770.31113321409
2.73-2.760.368710.30913661437
2.76-2.790.336750.2713211396
2.79-2.820.353540.27513171371
2.82-2.850.365650.29213321397
2.85-2.890.35840.29513561440
2.89-2.920.328850.27313361421
2.92-2.960.317800.25412801360
2.96-30.352670.27713421409
3-3.040.343760.26813471423
3.04-3.090.385680.26813411409
3.09-3.140.324660.2713201386
3.14-3.190.301890.26213181407
3.19-3.240.391810.24813351416
3.24-3.30.279780.22913461424
3.3-3.370.309620.25713051367
3.37-3.430.3730.24413381411
3.43-3.510.283630.22413801443
3.51-3.590.3850.22912841369
3.59-3.680.335740.23913681442
3.68-3.780.326810.24413301411
3.78-3.890.289780.22712981376
3.89-4.020.296700.23913711441
4.02-4.160.251800.21713181398
4.16-4.330.243540.19913681422
4.33-4.520.235690.19513191388
4.52-4.760.218800.17213561436
4.76-5.060.192660.18412981364
5.06-5.440.293620.20913551417
5.44-5.990.313800.23513371417
5.99-6.850.294640.22313521416
6.85-8.590.21630.19613091372
8.59-300.254360.206819855
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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