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- PDB-5vnh: Crystal structure of Sec23a/Sec24a/Sec22 complexed with a C-termi... -

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Basic information

Entry
Database: PDB / ID: 5vnh
TitleCrystal structure of Sec23a/Sec24a/Sec22 complexed with a C-terminal SV sorting motif
Components
  • (Protein transport protein ...) x 2
  • C-terminal SV motif
  • 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 / SNAP receptor activity / SNARE complex / COPII vesicle coat / negative regulation of autophagosome assembly ...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 / SNAP receptor activity / SNARE complex / COPII vesicle coat / negative regulation of autophagosome assembly / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / syntaxin binding / ER-Phagosome pathway / 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 / SNARE binding / cholesterol homeostasis / 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 / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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: 2.6 Å
AuthorsMa, W. / Goldberg, J.
Funding support United States, 1items
OrganizationGrant numberCountry
MSKCC United States
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
DepositionApr 30, 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
D: C-terminal SV motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,2986
Polymers189,1684
Non-polymers1312
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-15 kcal/mol
Surface area66230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.937, 96.895, 127.341
Angle α, β, γ (deg.)90.00, 91.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein transport protein ... , 2 types, 2 molecules AB

#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 / Cell line (production host): Hi-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15436
#2: Protein Protein transport protein Sec24A / SEC24-related protein A


Mass: 84336.820 Da / Num. of mol.: 1 / Fragment: UNP resiudes 346-1093
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24A / Cell line (production host): Hi-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O95486

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Protein / Protein/peptide , 2 types, 2 molecules CD

#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 resiudes 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: Protein/peptide C-terminal SV motif


Mass: 620.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 82 molecules

#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 52.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50mM HEPES PH 7.8, 0.5M NaAc 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: 2.6→48.881 Å / Num. obs: 61690 / % possible obs: 99.5 % / Redundancy: 4.2 % / Net I/σ(I): 2.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NUT

2nut


Resolution: 2.6→48.881 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 29.55
RfactorNum. reflection% reflection
Rfree0.2496 1927 3.27 %
Rwork0.2116 --
obs0.2129 58946 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12487 0 2 80 12569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212759
X-RAY DIFFRACTIONf_angle_d0.54117296
X-RAY DIFFRACTIONf_dihedral_angle_d12.2757775
X-RAY DIFFRACTIONf_chiral_restr0.0411953
X-RAY DIFFRACTIONf_plane_restr0.0042235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.32231390.2784068X-RAY DIFFRACTION100
2.665-2.73710.35851460.28424051X-RAY DIFFRACTION100
2.7371-2.81760.36691330.28064075X-RAY DIFFRACTION100
2.8176-2.90860.31551440.27414057X-RAY DIFFRACTION100
2.9086-3.01250.32461370.26024053X-RAY DIFFRACTION100
3.0125-3.13310.31231460.25644086X-RAY DIFFRACTION100
3.1331-3.27570.29771280.24384066X-RAY DIFFRACTION100
3.2757-3.44830.24541470.2314105X-RAY DIFFRACTION100
3.4483-3.66430.2471370.21314041X-RAY DIFFRACTION100
3.6643-3.94710.25421380.20164087X-RAY DIFFRACTION100
3.9471-4.34410.22491290.18144120X-RAY DIFFRACTION100
4.3441-4.97220.21141350.1724099X-RAY DIFFRACTION100
4.9722-6.26230.21041290.20144141X-RAY DIFFRACTION100
6.2623-48.88910.22361390.19763970X-RAY DIFFRACTION94
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)
13.94252.77930.69083.94210.23353.04-0.34860.2880.0878-0.61910.24130.51570.2233-0.30070.05390.5985-0.0241-0.22370.46740.11690.7737-43.069198.9657120.3899
22.4024-0.7880.84553.8424-1.26792.2111-0.1047-0.1677-0.1440.15370.0073-0.17550.0230.2120.05330.38310.13630.0010.43580.03990.5095-15.677586.5917149.8111
31.3581-0.06530.18932.7431-0.76931.9502-0.18380.16490.0825-0.17910.19150.0643-0.1129-0.0258-0.01970.35180.0106-0.07880.40910.02440.5549-27.1529107.3571130.3479
42.32390.60580.04234.6369-1.55971.41740.0971-0.65520.37892.52410.15470.7628-1.2845-0.3029-0.33181.74390.19850.08040.6841-0.05410.988-29.832121.3567153.5329
52.7624-1.37830.31332.4934-0.14631.0094-0.2665-0.5430.12810.35960.2494-0.1271-0.0161-0.0410.02040.50590.14620.02860.51490.0390.372315.751750.6847168.8094
62.0550.0194-0.06843.91720.80324.0329-0.0975-0.6113-0.80230.83190.0261.16030.5392-0.73880.10210.73650.04260.240.70230.26180.9819.184525.0666169.0712
72.96170.2358-0.1526.76110.73095.26320.2054-0.3632-0.18320.4819-0.14441.60930.4082-1.1432-0.12080.7264-0.00230.09420.78010.21041.22566.638924.5514167.1929
86.02241.07611.10283.4359-2.65038.8625-0.49560.6540.7283-0.30560.3407-0.0509-1.3888-1.10820.311.21340.3702-0.30651.1605-0.23370.836612.288382.9578178.9231
93.70050.115-0.96373.0522-1.54320.9987-0.47280.5875-0.0031-0.6603-0.1415-0.3502-1.0550.24940.47381.4850.0966-0.59950.9728-0.41321.109819.756582.3076180.7272
102.43250.5017-0.30120.43430.77237.3108-0.8911-0.13371.5837-1.21280.46210.8638-1.6664-0.13290.44543.00450.3305-1.25830.9929-0.24131.749116.290492.3852180.1037
118.84320.5427-2.55226.3167-2.81985.2149-0.5370.02721.4973-1.54940.56270.2692-1.7357-0.9360.13372.2170.3305-0.76660.7683-0.26081.314911.94588.8925179.8801
122.5968-0.4620.81215.1136-1.16160.47770.0067-1.11981.31810.035-0.77361.5027-0.9899-1.20550.74431.83830.6905-0.81341.7334-0.91291.65986.616384.8115188.7589
133.61482.3594-0.78896.0249-1.14722.3963-0.7583-1.36670.2430.545-1.06990.0969-0.3384-2.05281.68840.85640.3525-0.17181.0373-0.20260.674614.617570.9061188.8592
144.7295-4.80074.84894.8957-5.11869.77180.14380.65540.4203-0.4661-0.81320.24850.1909-0.91510.55211.40610.3815-0.21671.6139-0.5331.27263.238277.6419181.2502
158.98561.53320.48751.04780.21394.3683-1.00840.14722.0425-0.54010.23380.8809-2.6131-0.41330.59442.45170.0537-0.86341.1126-0.08851.65612.678592.1414176.3559
165.9663.14424.52322.27532.78623.73930.050.3807-2.27932.37981.3913-0.80510.42041.1736-1.43551.3690.0110.06721.2986-0.57971.294527.527663.5006175.3495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 379 )
3X-RAY DIFFRACTION3chain 'A' and (resid 380 through 607 )
4X-RAY DIFFRACTION4chain 'A' and (resid 608 through 764 )
5X-RAY DIFFRACTION5chain 'B' and (resid 346 through 881 )
6X-RAY DIFFRACTION6chain 'B' and (resid 882 through 1016 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1017 through 1093 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 9 )
9X-RAY DIFFRACTION9chain 'C' and (resid 10 through 50 )
10X-RAY DIFFRACTION10chain 'C' and (resid 51 through 66 )
11X-RAY DIFFRACTION11chain 'C' and (resid 67 through 80 )
12X-RAY DIFFRACTION12chain 'C' and (resid 81 through 105 )
13X-RAY DIFFRACTION13chain 'C' and (resid 106 through 112 )
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 123 )
15X-RAY DIFFRACTION15chain 'C' and (resid 124 through 157 )
16X-RAY DIFFRACTION16chain 'D' and (resid 77 through 79 )

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