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- PDB-7sul: Crystal structure of the WD-repeat domain of human SEC31A -

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Basic information

Entry
Database: PDB / ID: 7sul
TitleCrystal structure of the WD-repeat domain of human SEC31A
ComponentsProtein transport protein Sec31AProtein targeting
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / SEC31A / KIAA0905 / SEC31L1 / ABP125 / ABP130 / HSPC275 / HSPC334 / SGC / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


vesicle coat / COPII-coated vesicle cargo loading / COPII vesicle coat / XBP1(S) activates chaperone genes / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Signaling by ALK fusions and activated point mutants / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site ...vesicle coat / COPII-coated vesicle cargo loading / COPII vesicle coat / XBP1(S) activates chaperone genes / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Signaling by ALK fusions and activated point mutants / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / response to calcium ion / calcium-dependent protein binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / structural molecule activity / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Protein transport protein SEC31-like / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 / 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
Similarity search - Domain/homology
Protein transport protein Sec31A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsZeng, H. / Dong, A. / Loppnau, P. / Hutchinson, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal structure of the WD-repeat domain of human SEC31A
Authors: Zeng, H. / Dong, A. / Loppnau, P. / Hutchinson, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionNov 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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 Sec31A
B: Protein transport protein Sec31A
C: Protein transport protein Sec31A
D: Protein transport protein Sec31A


Theoretical massNumber of molelcules
Total (without water)157,5134
Polymers157,5134
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.180, 156.750, 85.190
Angle α, β, γ (deg.)90.000, 99.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein transport protein Sec31A / Protein targeting / ABP125 / ABP130 / SEC31-like protein 1 / SEC31-related protein A / Web1-like protein


Mass: 39378.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC31A, KIAA0905, SEC31L1, HSPC275, HSPC334 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94979
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.14 Å3/Da / Density % sol: 42.52 % / Mosaicity: 0.64 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30%(w/v)PEG4K,0.2M Sodium Acetat, 0.1M Tris HCL pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 49159 / % possible obs: 94.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 47.81 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.069 / Rrim(I) all: 0.136 / Χ2: 1.274 / Net I/σ(I): 7.1 / Num. measured all: 167966
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4430.78119940.70.4730.9170.6475
2.44-2.493.10.70921210.7230.4220.8280.63283.5
2.49-2.533.30.64922730.7460.3850.7570.62587.4
2.53-2.593.40.60423770.7940.3530.7020.6591
2.59-2.643.50.52824970.8480.3080.6130.67996.1
2.64-2.73.60.45825250.8830.2660.5310.70996.4
2.7-2.773.70.39625070.9070.230.4590.75797.4
2.77-2.853.70.32926080.9430.1920.3820.78498.7
2.85-2.933.70.26125220.9580.1530.3030.8598.6
2.93-3.023.60.23225900.9610.1360.270.96798.1
3.02-3.133.50.19225510.9690.1140.2251.08798.5
3.13-3.263.40.15525340.9730.0950.1831.25797.8
3.26-3.413.10.13124500.9830.0810.1551.48193
3.41-3.583.40.10224640.9880.0610.1191.75895
3.58-3.813.60.08925450.990.0530.1041.83797.3
3.81-4.13.50.07924910.9910.0470.0922.0196
4.1-4.523.30.06325010.9930.0380.0742.02795.5
4.52-5.173.20.06125200.9930.0380.0722.33195.7
5.17-6.513.20.0625340.9910.0380.0722.20196.4
6.51-503.60.05225550.9960.0310.0612.08895.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.81 Å48.05 Å
Translation3.81 Å48.05 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.8.3phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
HKL-3000data processing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALPHAFOLD

Resolution: 2.4→44.37 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.485 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.426 / SU Rfree Blow DPI: 0.25 / SU Rfree Cruickshank DPI: 0.261
RfactorNum. reflection% reflectionSelection details
Rfree0.237 986 2.01 %RANDOM
Rwork0.189 ---
obs0.19 49130 93.7 %-
Displacement parametersBiso max: 134.35 Å2 / Biso mean: 53.22 Å2 / Biso min: 22.48 Å2
Baniso -1Baniso -2Baniso -3
1--18.4573 Å20 Å24.5569 Å2
2--1.4622 Å20 Å2
3---16.995 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.4→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9945 0 0 69 10014
Biso mean---44.19 -
Num. residues----1330
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3289SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1723HARMONIC5
X-RAY DIFFRACTIONt_it10200HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1404SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10803SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10200HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13946HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion19.31
LS refinement shellResolution: 2.4→2.41 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2942 21 2.09 %
Rwork0.2317 982 -
obs--62.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.80730.23390.50012.74310.51833.2678-0.0874-0.0309-0.0114-0.2046-0.0579-0.0013-0.2337-0.47750.1453-0.12620.0252-0.0558-0.0605-0.046-0.2049-1.13295.77634.3581
22.30120.85540.51482.150.88782.1923-0.0122-0.0273-0.0718-0.1032-0.05090.07970.05090.02270.063-0.08490.0465-0.048-0.1285-0.027-0.1056-21.4865-11.7694-29.4981
31.6-0.2574-0.18513.2213-1.16013.87170.0998-0.08850.2137-0.35220.0072-0.06320.04980.0856-0.107-0.0836-0.0608-0.044-0.17230.0121-0.2206-20.4363-37.721312.7778
41.3985-0.42580.66983.20910.06513.6296-0.02440.0180.0390.1397-0.04120.085-0.30770.10610.0656-0.0602-0.0048-0.0529-0.12920.0506-0.259-9.6815-54.7988-34.5565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-1 - A|334 }A-1 - 334
2X-RAY DIFFRACTION2{ B|-1 - B|334 }B-1 - 334
3X-RAY DIFFRACTION3{ C|-1 - C|334 }C-1 - 334
4X-RAY DIFFRACTION4{ D|0 - D|334 }D0 - 334

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