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

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Basic information

Entry
Database: PDB / ID: 5vni
TitleCrystal structure of Sec23a/Sec24a/Sec22 complexed with a C-terminal FA sorting motif
Components
  • (Protein transport protein ...) x 2
  • C-terminal FA
  • 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 / COPII-mediated vesicle transport / syntaxin binding / 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 / positive regulation of protein secretion / protein localization to plasma membrane / 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 / Gelsolin-like domain superfamily / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / 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: 2.788 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 FA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,2016
Polymers189,0704
Non-polymers1312
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-53 kcal/mol
Surface area65850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.606, 96.065, 129.998
Angle α, β, γ (deg.)90.00, 90.06, 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 residues 346-109
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 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: Protein/peptide C-terminal FA


Mass: 523.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 47 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.: 45 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
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: 2.7876→48.803 Å / Num. obs: 40031 / % possible obs: 98.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.083 / Χ2: 2.57 / Net I/σ(I): 12.6
Reflection shellResolution: 2.7876→2.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 1 / Num. unique obs: 3587 / CC1/2: 0.67 / Rpim(I) all: 0.427 / Χ2: 0.516 / % possible all: 98.2

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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: 2.788→48.803 Å / SU ML: 0.44 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 2001 5 %
Rwork0.2119 --
obs0.2147 40031 87.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.788→48.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12468 0 2 45 12515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212752
X-RAY DIFFRACTIONf_angle_d0.48117277
X-RAY DIFFRACTIONf_dihedral_angle_d11.6097763
X-RAY DIFFRACTIONf_chiral_restr0.041951
X-RAY DIFFRACTIONf_plane_restr0.0042232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7876-2.85730.3635970.30641749X-RAY DIFFRACTION57
2.8573-2.93450.36051280.31072585X-RAY DIFFRACTION84
2.9345-3.02090.3531480.30112708X-RAY DIFFRACTION88
3.0209-3.11840.34041510.2812757X-RAY DIFFRACTION90
3.1184-3.22980.32621480.26462833X-RAY DIFFRACTION92
3.2298-3.35910.3321530.25312800X-RAY DIFFRACTION92
3.3591-3.51190.30431450.24162798X-RAY DIFFRACTION90
3.5119-3.6970.29761540.22952887X-RAY DIFFRACTION95
3.697-3.92860.28381590.21462921X-RAY DIFFRACTION94
3.9286-4.23170.24411480.18862838X-RAY DIFFRACTION92
4.2317-4.65730.22411410.17842761X-RAY DIFFRACTION89
4.6573-5.33050.23131490.18362836X-RAY DIFFRACTION92
5.3305-6.71310.28131420.21042786X-RAY DIFFRACTION89
6.7131-48.81080.23421380.18572771X-RAY DIFFRACTION87
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)
15.85641.8286-1.69082.0323-0.38444.67510.10760.4475-0.02750.17690.1021-0.04260.14680.6523-0.03290.59510.10990.03170.7341-0.09040.562731.9301-108.6469-2.5247
24.78762.0341-2.28237.2583-1.37555.2055-0.49630.7061-0.2755-0.6592-0.0489-0.95420.28430.1390.41190.89080.00470.24820.7415-0.09050.996642.196-94.8769-13.2954
33.9973-0.3071-1.68923.56981.94122.83940.1966-0.18670.63960.00570.0050.2337-0.08330.0391-0.21640.37980.0819-0.01620.52060.00150.512114.5902-82.817925.5503
41.0015-0.3936-0.65092.2850.31642.6722-0.0871-0.0281-0.1777-0.11230.03140.20980.1161-0.06530.07070.57540.04260.05670.7224-0.06160.826812.1531-96.528315.7946
52.37711.78130.85447.23070.76542.20810.0540.26440.1347-1.07930.0350.36430.09720.1286-0.12770.61690.0699-0.01790.6086-0.04140.536721.8622-109.4085-1.7443
61.7003-0.57740.39052.37711.23892.7234-0.0585-0.0102-0.16740.1427-0.00870.3460.43310.14120.05050.7007-0.01050.21390.5321-0.04040.835920.4332-123.508313.9755
72.7275-0.14960.46254.35010.86134.26280.1173-0.81840.05360.8144-0.2357-0.15880.378-0.19990.15350.5912-0.0480.1580.71590.01460.955223.469-123.883128.4922
82.2266-0.5553-0.22861.8644-0.00171.2304-0.1274-0.1202-0.30030.0518-0.0333-0.02390.13440.05290.18270.4560.05840.0440.44360.04580.6414-15.1344-54.154842.6975
92.0857-1.48570.43153.295-0.88611.306-0.08320.0568-0.04150.01110.11050.4381-0.1607-0.3053-0.03050.43870.07550.02210.59240.03040.6914-30.8454-44.307442.5425
104.16590.52321.64690.55660.44872.6174-0.17210.21110.6177-0.19750.0858-0.0936-0.29460.25250.09140.61370.02460.05710.60750.10140.7845-10.4968-26.967943.154
113.67160.16612.24391.939-0.6932.8721-0.170.3820.4813-0.4348-0.104-0.3068-0.03880.34030.21790.66580.02350.03980.67070.04890.6008-7.9965-26.609741.2515
126.2379-0.94660.1452.48711.56862.5835-0.91731.21250.7155-0.6297-0.2801-0.30230.15820.22160.60381.0926-0.07580.64920.94440.30771.0685-16.9494-84.445952.1772
130.6133-0.03580.88585.03452.05412.1101-0.2103-0.15740.02020.62070.26540.12091.16020.2434-0.06860.90490.29820.32940.70.2121.063-18.9149-79.258952.2435
142.0297-1.11231.56242.03111.06825.50710.20660.65680.773-0.1882-0.37220.3533-0.4099-1.05650.27091.04330.15720.39291.02630.2841.3121-27.2301-86.043354.6237
156.9333.4064-6.41338.5559-3.59615.9552-0.32071.48-1.9884-0.33660.3921-0.52821.4366-1.7465-0.12981.4767-0.44360.61421.0439-0.41371.7103-22.9109-95.778150.7206
168.4773-0.05640.61217.4804-0.09694.8279-0.31750.0549-1.6877-1.273-0.0969-0.8504-0.18310.640.36370.94520.15270.34860.68070.08591.1184-14.1347-90.135856.2065
174.22581.46460.43383.72094.50697.64270.6726-0.41030.23390.7664-0.5692-0.4057-0.72210.0784-0.05990.99340.00520.25920.79560.24291.2438-17.1907-74.85565.6462
185.5287-0.0463-1.45963.06421.48626.982-0.995-0.0199-0.8698-0.98831.7041-0.83960.54370.5636-0.71711.06360.13760.3920.94640.15731.3513-7.2928-85.562151.4322
195.4208-5.5701-4.79345.77415.01154.4093-0.53811.2249-2.1436-0.89170.73550.01251.4906-3.0531-0.06241.4968-0.54170.29062.3086-0.081.4238-30.7524-94.543650.4936
200.11350.2432-0.04950.6816-0.14410.0296-0.05230.17810.1319-0.37560.0195-0.3271-0.20060.03780.01522.0634-0.1292-0.08370.97590.3591.5778-31.0911-65.598449.6397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 263 )
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 430 )
5X-RAY DIFFRACTION5chain 'A' and (resid 431 through 557 )
6X-RAY DIFFRACTION6chain 'A' and (resid 558 through 646 )
7X-RAY DIFFRACTION7chain 'A' and (resid 647 through 764 )
8X-RAY DIFFRACTION8chain 'B' and (resid 348 through 763 )
9X-RAY DIFFRACTION9chain 'B' and (resid 764 through 881 )
10X-RAY DIFFRACTION10chain 'B' and (resid 882 through 1016 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1017 through 1093 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 9 )
13X-RAY DIFFRACTION13chain 'C' and (resid 10 through 29 )
14X-RAY DIFFRACTION14chain 'C' and (resid 30 through 50 )
15X-RAY DIFFRACTION15chain 'C' and (resid 51 through 58 )
16X-RAY DIFFRACTION16chain 'C' and (resid 59 through 99 )
17X-RAY DIFFRACTION17chain 'C' and (resid 100 through 112 )
18X-RAY DIFFRACTION18chain 'C' and (resid 113 through 149 )
19X-RAY DIFFRACTION19chain 'C' and (resid 150 through 157 )
20X-RAY DIFFRACTION20chain 'D' and (resid 101 through 103 )

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