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- PDB-5vno: Crystal structure of Sec23a/Sec24a/Sec22 -

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Basic information

Entry
Database: PDB / ID: 5vno
TitleCrystal structure of Sec23a/Sec24a/Sec22
Components
  • Protein transport protein Sec23A
  • Protein transport protein Sec24A
  • Vesicle-trafficking protein SEC22b
KeywordsPROTEIN TRANSPORT / COPII / Trafficking / p24 / ER retention
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / COPI-coated vesicle / regulation of cholesterol transport / COPI-dependent Golgi-to-ER retrograde traffic / COPII-coated vesicle cargo loading / COPII vesicle coat / negative regulation of autophagosome assembly / SNAP receptor activity / SNARE complex ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPI-coated vesicle / regulation of cholesterol transport / COPI-dependent Golgi-to-ER retrograde traffic / COPII-coated vesicle cargo loading / COPII vesicle coat / negative regulation of autophagosome assembly / SNAP receptor activity / SNARE complex / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / ER-Phagosome pathway / syntaxin binding / COPII-mediated vesicle transport / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / GTPase activator activity / cholesterol homeostasis / SNARE binding / protein localization to plasma membrane / positive regulation of protein secretion / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / positive regulation of protein catabolic process / synaptic vesicle / melanosome / protein transport / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / endoplasmic reticulum / zinc ion binding / cytosol
Similarity search - Function
Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Protein transport protein Sec23 / Sec23, C-terminal ...Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Protein transport protein Sec23 / Sec23, C-terminal / : / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Gelsolin-like domain superfamily / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / Longin-like domain superfamily / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor, type A domain / Beta-Lactamase / von Willebrand factor A-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vesicle-trafficking protein SEC22b / Protein transport protein Sec24A / Protein transport protein Sec23A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.905 Å
AuthorsMa, W. / Goldberg, J.
CitationJournal: Elife / Year: 2017
Title: ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate.
Authors: Ma, W. / Goldberg, E. / Goldberg, J.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein transport protein Sec23A
B: Protein transport protein Sec24A
C: Vesicle-trafficking protein SEC22b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,6785
Polymers188,5473
Non-polymers1312
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.046, 96.727, 126.796
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein transport protein Sec23A / SEC23-related protein A


Mass: 86178.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q15436
#2: Protein Protein transport protein Sec24A / SEC24-related protein A


Mass: 84336.820 Da / Num. of mol.: 1 / Fragment: UNP residues 346-1093
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24A
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O95486
#3: Protein Vesicle-trafficking protein SEC22b / ER-Golgi SNARE of 24 kDa / ERS24 / SEC22 vesicle-trafficking protein homolog B / SEC22 vesicle- ...ER-Golgi SNARE of 24 kDa / ERS24 / SEC22 vesicle-trafficking protein homolog B / SEC22 vesicle-trafficking protein-like 1 / mSec22b


Mass: 18031.645 Da / Num. of mol.: 1 / Fragment: UNP residues 1-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sec22b, Sec22l1 / Production host: Escherichia coli (E. coli) / References: UniProt: O08547
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50mM HEPES PH 7.8, 0.5M NaCl and 12% PEG4K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 42151 / % possible obs: 98.6 % / Redundancy: 3.6 % / Net I/σ(I): 15.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NUT

2nut


Resolution: 2.905→49.94 Å / SU ML: 0.47 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 34.66
RfactorNum. reflection% reflection
Rfree0.2984 2017 4.79 %
Rwork0.2437 --
obs0.2464 42151 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.905→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12443 0 2 62 12507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512721
X-RAY DIFFRACTIONf_angle_d0.59517234
X-RAY DIFFRACTIONf_dihedral_angle_d12.2127746
X-RAY DIFFRACTIONf_chiral_restr0.0431951
X-RAY DIFFRACTIONf_plane_restr0.0042227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9047-2.97740.39811380.34452698X-RAY DIFFRACTION95
2.9774-3.05790.38321360.34482876X-RAY DIFFRACTION100
3.0579-3.14780.38241410.33772837X-RAY DIFFRACTION100
3.1478-3.24940.30771500.30512879X-RAY DIFFRACTION100
3.2494-3.36550.33471400.29252856X-RAY DIFFRACTION100
3.3655-3.50020.34171360.27242865X-RAY DIFFRACTION100
3.5002-3.65950.32721480.27172863X-RAY DIFFRACTION100
3.6595-3.85240.30431540.25742899X-RAY DIFFRACTION100
3.8524-4.09360.29191420.23252853X-RAY DIFFRACTION100
4.0936-4.40950.22711390.20752899X-RAY DIFFRACTION100
4.4095-4.85290.24711600.19642866X-RAY DIFFRACTION100
4.8529-5.55440.28171470.2192877X-RAY DIFFRACTION100
5.5544-6.99490.31681420.24992905X-RAY DIFFRACTION100
6.9949-49.94760.30131440.21842961X-RAY DIFFRACTION99
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)
15.34841.2085-4.86294.7358-2.6528.60950.18460.23610.14440.4066-0.0145-0.043-0.8003-0.2126-0.12920.5544-0.0711-0.28460.5111-0.0040.7919-32.0078115.528-4.7094
26.87575.46721.64826.47383.56743.2735-0.35410.5099-0.5205-0.94650.22370.23540.3939-0.42970.10540.8563-0.029-0.31010.4920.03921.0023-42.67194.3992-8.5594
33.8218-2.62172.00623.5096-2.2722.88820.1691-0.2808-0.9295-0.07950.32720.38520.3059-0.0393-0.52380.42230.12770.03280.46330.04490.644-20.47485.745921.8327
45.5939-0.27250.42227.1905-0.03344.192-0.1446-0.2525-0.5930.75320.25260.06680.46710.2074-0.03320.67820.2873-0.09650.54650.2430.8637-12.188881.374927.4275
51.9078-0.44921.25532.4948-0.22972.6502-0.14040.0199-0.05210.1130.0961-0.2839-0.03190.35650.08120.44860.0733-0.08890.43130.04080.7048-14.74297.225213.3143
62.66290.71190.93613.21360.05321.6774-0.29610.27270.0717-0.59410.30710.7025-0.0388-0.4146-0.31780.6053-0.027-0.31670.64560.06880.957-32.3403106.2422-4.382
72.79370.98760.75346.319-2.41024.0263-0.19440.19380.44010.07920.0581-0.3306-0.42460.18450.1830.53490.0142-0.18010.4451-0.02860.8325-17.6009121.74025.2401
82.37830.6547-1.29821.1207-2.09095.5196-0.114-0.14640.85842.54850.83710.655-1.68190.366-0.53761.98430.33190.01270.5466-0.03581.2169-28.8384123.628526.533
91.32290.3291-1.21147.4939-2.68983.07740.0472-0.47080.27651.58490.19090.5643-0.91840.1996-0.31140.86270.0674-0.31290.75050.07111.03-20.938123.679919.8858
103.6104-0.95560.51681.3433-0.00792.255-0.2404-0.7866-0.71920.9010.5726-0.46960.6717-0.382-0.01341.07870.3005-0.10880.92720.25640.888233.368633.319549.6891
114.1142-1.26430.81131.67181.11061.8788-0.6792-1.68821.09530.45740.5594-0.6442-0.44040.1335-0.15191.09570.3962-0.39571.254-0.2621.024236.527755.968256.9855
124.6993-1.01731.65265.2166-1.18763.5035-0.3086-0.41920.3760.23190.03330.3561-0.2696-0.20520.17110.45160.227-0.00310.54440.01140.5963-0.091266.08537.7334
133.0954-1.2805-0.29882.9423-0.32091.4745-0.1416-0.0821-0.0664-0.08640.13530.1870.0186-0.18470.0220.46910.1401-0.06940.4390.04450.465812.458353.141932.2172
142.8978-0.84820.16213.89641.03782.0472-0.3226-0.6463-0.08840.23080.3964-0.381-0.12650.11850.00950.61050.177-0.08280.67330.05280.557731.38250.027243.154
153.1111-0.07820.95954.82060.39834.0218-0.0033-0.1926-0.71830.35570.05030.21010.22060.0610.02110.61790.1080.00830.42280.13980.660723.030132.268835.9827
167.0438-1.0765-0.91873.1143-0.37611.3565-0.6301-0.3184-0.98011.840.1077-0.77360.642-0.40320.18921.1039-0.03480.22890.79220.20640.97994.447522.652346.3837
175.4293-0.755-2.80845.55192.57336.0837-0.131-0.4742-1.79250.4295-0.37161.54890.5021-0.43860.3740.73540.07350.05990.70030.24181.289310.388827.669339.7621
182.23261.2780.56912.7587-1.01092.58040.8736-0.2308-0.87391.93310.5773-0.2291.4303-0.3653-1.02370.98760.2795-0.50670.9925-0.29570.995618.250883.599655.2396
197.82582.0830.53373.8701-1.95191.188-0.48651.1774-0.61060.37640.1991-1.3087-0.08831.4528-0.13131.66330.0419-0.45821.0244-0.35081.240224.301186.437351.5952
206.39822.5344-2.77194.631-3.77073.1157-1.0532-0.05422.5702-1.0030.59691.7449-1.8027-0.310.43112.33580.2508-0.84751.0448-0.20051.649320.086895.352552.5895
217.83271.0158-1.13583.41574.06335.5773-0.9407-0.8992.2812-1.28780.18960.3854-1.0049-1.71280.47111.37420.3957-0.4341.3201-0.32791.431211.681790.851856.2516
222.97661.7575-1.33264.29692.08933.12150.332-0.9314-0.39480.6788-1.61040.00340.60690.0020.93121.04980.3147-0.24911.317-0.27680.853317.12576.079964.868
237.70493.7101-3.98998.99911.03443.3159-0.39751.09780.6469-0.87890.33770.9625-1.1391-2.05720.37081.28790.353-0.31471.5429-0.35091.24286.923480.651853.7089
242.45072.454-4.89183.0054-5.00589.80571.57921.05740.7665-0.20470.8836-1.3328-1.985-1.1449-1.16821.47270.4175-0.79911.1854-0.56612.30024.717194.487947.5855
253.81932.2327-1.03721.3015-0.61230.2820.62510.40891.1578-0.5299-0.16430.7047-2.63671.42710.0592.4977-0.42140.00081.7761-0.54750.740529.611796.918250.3951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 196 )
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 263 )
5X-RAY DIFFRACTION5chain 'A' and (resid 264 through 455 )
6X-RAY DIFFRACTION6chain 'A' and (resid 456 through 518 )
7X-RAY DIFFRACTION7chain 'A' and (resid 519 through 607 )
8X-RAY DIFFRACTION8chain 'A' and (resid 608 through 686 )
9X-RAY DIFFRACTION9chain 'A' and (resid 687 through 764 )
10X-RAY DIFFRACTION10chain 'B' and (resid 346 through 396 )
11X-RAY DIFFRACTION11chain 'B' and (resid 397 through 491 )
12X-RAY DIFFRACTION12chain 'B' and (resid 492 through 628 )
13X-RAY DIFFRACTION13chain 'B' and (resid 629 through 763 )
14X-RAY DIFFRACTION14chain 'B' and (resid 764 through 859 )
15X-RAY DIFFRACTION15chain 'B' and (resid 860 through 958 )
16X-RAY DIFFRACTION16chain 'B' and (resid 959 through 1016 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1017 through 1093 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 19 )
19X-RAY DIFFRACTION19chain 'C' and (resid 20 through 50 )
20X-RAY DIFFRACTION20chain 'C' and (resid 51 through 66 )
21X-RAY DIFFRACTION21chain 'C' and (resid 67 through 99 )
22X-RAY DIFFRACTION22chain 'C' and (resid 100 through 112 )
23X-RAY DIFFRACTION23chain 'C' and (resid 113 through 123 )
24X-RAY DIFFRACTION24chain 'C' and (resid 124 through 149 )
25X-RAY DIFFRACTION25chain 'C' and (resid 150 through 157 )

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