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- PDB-3mzl: Sec13/Sec31 edge element, loop deletion mutant -

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Basic information

Entry
Database: PDB / ID: 3mzl
TitleSec13/Sec31 edge element, loop deletion mutant
Components
  • Protein transport protein SEC13Protein targeting
  • Protein transport protein SEC31Protein targeting
KeywordsPROTEIN TRANSPORT / alpha-helical-stack / beta-propeller
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 - #980 / Helix Hairpins - #1600 / 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 / Sec23-binding domain of Sec16 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #980 / Helix Hairpins - #1600 / 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 / Sec23-binding domain of Sec16 / Sec13/Seh1 family / N-terminal domain of TfIIb / Helix Hairpins / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Single Sheet / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWhittle, J.R. / Schwartz, T.U.
CitationJournal: J.Cell Biol. / Year: 2010
Title: Structure of the Sec13-Sec16 edge element, a template for assembly of the COPII vesicle coat.
Authors: Whittle, J.R. / Schwartz, T.U.
History
DepositionMay 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein transport protein SEC13
B: Protein transport protein SEC31
C: Protein transport protein SEC13
D: Protein transport protein SEC31
E: Protein transport protein SEC13
F: Protein transport protein SEC31
G: Protein transport protein SEC13
H: Protein transport protein SEC31


Theoretical massNumber of molelcules
Total (without water)287,1028
Polymers287,1028
Non-polymers00
Water0
1
A: Protein transport protein SEC13
B: Protein transport protein SEC31
C: Protein transport protein SEC13
D: Protein transport protein SEC31


Theoretical massNumber of molelcules
Total (without water)143,5514
Polymers143,5514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19710 Å2
ΔGint-149 kcal/mol
Surface area54220 Å2
MethodPISA
2
E: Protein transport protein SEC13
F: Protein transport protein SEC31
G: Protein transport protein SEC13
H: Protein transport protein SEC31


Theoretical massNumber of molelcules
Total (without water)143,5514
Polymers143,5514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19430 Å2
ΔGint-147 kcal/mol
Surface area54390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.220, 46.620, 192.000
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 1410
2114C2 - 1410
3114E2 - 1410
4114G2 - 1410
1124B2 - 1000
2124D2 - 1000
3124F2 - 1000
4124H2 - 1000

NCS ensembles :
ID
1
2

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Components

#1: Protein
Protein transport protein SEC13 / Protein targeting


Mass: 33082.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ANU3, L8167.4, SEC13, YLR208W / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q04491
#2: Protein
Protein transport protein SEC31 / Protein targeting / Protein WEB1


Mass: 38692.414 Da / Num. of mol.: 4
Fragment: UNP residues 370-746, deletion of residues 474-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: D1229, SEC31, WEB1, YDL195W / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P38968

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.1mM bis-Tris propane, 0.2M sodium citrate, 16% polyethylene glycol 3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.772
11-h,-k,l20.228
ReflectionResolution: 2.8→30 Å / Num. obs: 69366 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.477 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.38 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.842 / SU B: 19.803 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29962 1792 2.6 %RANDOM
Rwork0.26715 ---
obs0.26801 67561 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.777 Å2
Baniso -1Baniso -2Baniso -3
1-43.29 Å20 Å23.26 Å2
2---19.49 Å20 Å2
3----23.81 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19212 0 0 0 19212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02219597
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9361.94526580
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90452412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10625.43884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.344153442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.451568
X-RAY DIFFRACTIONr_chiral_restr0.0590.22999
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114588
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5121.512072
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.938219463
X-RAY DIFFRACTIONr_scbond_it0.60237525
X-RAY DIFFRACTIONr_scangle_it1.1394.57117
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2196MEDIUM POSITIONAL0.210.5
12C2196MEDIUM POSITIONAL0.220.5
13E2196MEDIUM POSITIONAL0.230.5
14G2196MEDIUM POSITIONAL0.230.5
11A2196MEDIUM THERMAL0.162
12C2196MEDIUM THERMAL0.192
13E2196MEDIUM THERMAL0.182
14G2196MEDIUM THERMAL0.182
21B2596MEDIUM POSITIONAL0.360.5
22D2596MEDIUM POSITIONAL0.370.5
23F2596MEDIUM POSITIONAL0.380.5
24H2596MEDIUM POSITIONAL0.370.5
21B2596MEDIUM THERMAL0.122
22D2596MEDIUM THERMAL0.122
23F2596MEDIUM THERMAL0.122
24H2596MEDIUM THERMAL0.122

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