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- PDB-5vne: Crystal structure of Sec23a/Sec24a/Sec22 complexed with Emp24 sor... -

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Basic information

Entry
Database: PDB / ID: 5vne
TitleCrystal structure of Sec23a/Sec24a/Sec22 complexed with Emp24 sorting motif
Components
  • (Protein transport protein ...Protein targeting) x 2
  • EMP24
  • Vesicle-trafficking protein SEC22b
KeywordsPROTEIN TRANSPORT / COPII / Trafficking / Emp24 / ER retention
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / COPI-coated vesicle / regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPI-dependent Golgi-to-ER retrograde traffic / COPII vesicle coat / negative regulation of autophagosome assembly / SNARE complex ...Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / COPI-coated vesicle / regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPI-dependent Golgi-to-ER retrograde traffic / COPII vesicle coat / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-mediated vesicle transport / ER-Phagosome pathway / syntaxin binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / vesicle-mediated transport / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / melanosome / synaptic vesicle / protein transport / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / 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 / von Willebrand factor, type A domain / ADF-H/Gelsolin-like domain superfamily / 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)
Moesziomyces aphidis DSM 70725 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.698 Å
AuthorsMa, W. / Goldberg, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Memorial Sloan Kettering Cancer Center 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 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 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: EMP24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,9956
Polymers188,8644
Non-polymers1312
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-21 kcal/mol
Surface area66460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.757, 96.501, 126.574
Angle α, β, γ (deg.)90.00, 91.63, 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 / Protein targeting / 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 / Protein targeting / 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 / 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 EMP24


Mass: 317.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Moesziomyces aphidis DSM 70725 (fungus)

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Non-polymers , 2 types, 100 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 / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
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: 2.698→50 Å / Num. obs: 52341 / % possible obs: 99.8 % / Redundancy: 4 % / Net I/σ(I): 2.6

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Processing

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

2nut


Resolution: 2.698→49.802 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 2013 3.85 %
Rwork0.2244 --
obs0.2261 52341 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.698→49.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12470 0 2 98 12570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212769
X-RAY DIFFRACTIONf_angle_d0.54617309
X-RAY DIFFRACTIONf_dihedral_angle_d14.6827780
X-RAY DIFFRACTIONf_chiral_restr0.0411955
X-RAY DIFFRACTIONf_plane_restr0.0042236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6976-2.7650.38181350.32193492X-RAY DIFFRACTION98
2.765-2.83980.321370.3033600X-RAY DIFFRACTION100
2.8398-2.92330.34461470.29023574X-RAY DIFFRACTION100
2.9233-3.01770.33481480.27673578X-RAY DIFFRACTION100
3.0177-3.12550.31161280.27193599X-RAY DIFFRACTION100
3.1255-3.25060.30491510.25953568X-RAY DIFFRACTION100
3.2506-3.39850.341400.24523599X-RAY DIFFRACTION100
3.3985-3.57760.28591530.23793593X-RAY DIFFRACTION100
3.5776-3.80170.26751410.22663579X-RAY DIFFRACTION100
3.8017-4.09510.23581430.20733620X-RAY DIFFRACTION100
4.0951-4.5070.22791500.18113586X-RAY DIFFRACTION100
4.507-5.15860.21861490.18643630X-RAY DIFFRACTION100
5.1586-6.4970.25951490.22323622X-RAY DIFFRACTION100
6.497-49.81050.24151420.20393688X-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)
13.440.8266-3.72612.83940.73547.7566-0.03110.46830.0924-0.0583-0.25870.1539-1.0202-0.3220.22230.5187-0.0062-0.28760.47170.17630.7776125.8409115.3739-4.694
28.65894.33962.86763.93692.72774.1684-0.55470.5908-0.233-0.86940.24340.56050.1174-0.69650.21650.7117-0.1144-0.26220.43460.09870.9157114.977994.5175-8.498
34.7713-2.91252.17913.9092-1.89572.03020.0169-0.3274-0.66920.05230.26210.35410.2789-0.0828-0.30890.33710.09380.08230.36550.09930.5402137.185885.744521.9078
41.5883-0.68050.68282.5853-1.20542.3705-0.20350.006-0.070.03280.0930.0030.0740.17380.07770.28240.0589-0.02750.33720.02540.609140.260496.230612.548
52.45940.69920.2524.8756-1.9563.7210.0154-0.20760.4030.94130.10110.1832-0.7896-0.0336-0.15080.58830.0688-0.09940.3035-0.0420.6889136.2061122.581513.4001
60.9489-0.46720.43673.86760.44050.3758-0.1112-0.30350.17132.05120.24410.7878-0.7353-0.3022-0.11411.3470.1656-0.01790.59550.00480.9844132.5255124.244826.6708
72.81041.08141.03232.77033.54534.4958-0.0993-0.712-0.61840.76190.3518-0.68370.5085-0.3026-0.29870.97530.2448-0.10030.75860.28870.8459189.592731.06550.8227
85.0830.0565-0.24392.097-0.39881.3205-0.2399-1.06960.88280.73310.2196-0.6784-0.09320.18570.00840.71520.3007-0.26490.7207-0.07090.6543194.004152.303952.3412
93.7878-1.75550.77312.7465-0.18382.0329-0.3674-0.7270.45830.61970.3997-0.1388-0.02880.01720.07850.50120.26760.00470.575-0.04770.4642168.626463.590645.2407
102.7154-1.02580.43012.5319-0.17151.2224-0.1549-0.14510.056-0.03070.0870.3503-0.1434-0.19510.02910.38160.16950.02640.38830.06270.4389165.942757.176133.0965
114.7206-2.0635-0.38765.32650.88732.7672-0.3234-0.16340.29480.17140.185-0.4767-0.40250.12930.19360.53130.1564-0.14540.4597-0.00870.533187.85255.71844.4928
122.3192-0.38630.95813.49460.39542.1843-0.2023-0.3371-0.49840.18720.17490.08350.2323-0.01130.03520.45590.18870.05760.40520.12910.4658183.685135.87137.7358
135.5898-0.085-1.48192.9752-1.34514.5876-0.3336-0.2609-1.68561.37980.21741.21591.3732-0.78570.13991.0812-0.11360.29440.67240.35021.3757162.250122.473446.3932
143.1448-0.1166-1.22615.191.71676.17760.098-0.348-0.91010.3897-0.28531.21740.4987-1.02830.21090.54320.01380.08120.62530.29031.0817168.089527.752539.8095
153.42783.5188-1.86855.5250.57788.5851-0.3705-0.46280.5680.01640.3717-0.3229-0.8818-0.8410.12191.0760.4316-0.54070.7776-0.37570.8994175.633583.611355.0094
163.1255-0.35182.00266.0036-0.65239.24030.28250.4465-0.096-1.00751.4257-1.5757-0.21110.376-1.59933.16720.23760.04341.1246-0.47511.9354172.448780.65940.8156
178.42890.0665-4.88718.39621.91727.6524-0.95850.53970.7651-0.3686-0.5378-0.6261-0.5175-0.81821.26711.4695-0.0675-0.43870.6764-0.13570.9995183.801388.048953.8723
184.1843-3.1751-1.96453.78343.3784.2419-0.36180.64950.9995-0.8126-0.0238-0.15110.45910.2270.26133.58130.1542-1.81861.19140.16112.2015178.882897.545150.6741
194.8603-0.8228-0.67573.12331.3740.6307-0.13430.25850.6579-2.60850.23071.55270.2408-0.29250.03642.68230.7226-1.29371.05-0.35181.9649175.965793.493254.2658
203.0038-2.1203-0.95778.24570.34610.78710.31490.33780.4591-2.375-0.1980.4212-0.2932-0.0850.10372.00590.7088-1.06060.1913-0.26971.6138173.377891.688552.2204
215.02512.2460.38623.02851.0421.2391-0.0076-1.0021.4067-1.8491-1.11882.2115-0.1704-0.69221.04211.5340.7463-0.48931.4542-0.89631.6714166.295190.864258.9416
224.09731.7298-4.2640.9457-1.47374.93-0.3898-1.18730.22390.338-0.97870.8174-0.2031-1.24651.04881.11210.4221-0.32961.24-0.58250.9192174.029276.258265.0349
238.6386-4.48878.27477.4999-3.18228.3195-1.951-0.30681.4954-0.44471.4371-0.4858-1.8667-0.44840.44611.30170.2299-0.52341.3136-0.40561.3249163.927981.198853.0095
243.08962.8536-2.08214.8617-1.68621.4240.01281.08021.4709-0.3372-0.1991.2861-1.0979-0.06060.0731.8089-0.0868-0.69891.0943-0.22491.4728174.729795.888248.8602
250.89021.2497-2.48771.7496-3.48696.94470.458-1.0578-1.25161.0456-0.4967-2.0957-0.23861.51130.05390.55610.0271-0.42210.9128-0.34851.4788188.901266.861247.6989
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 518 )
5X-RAY DIFFRACTION5chain 'A' and (resid 519 through 669 )
6X-RAY DIFFRACTION6chain 'A' and (resid 670 through 764 )
7X-RAY DIFFRACTION7chain 'B' and (resid 346 through 385 )
8X-RAY DIFFRACTION8chain 'B' and (resid 386 through 451 )
9X-RAY DIFFRACTION9chain 'B' and (resid 452 through 575 )
10X-RAY DIFFRACTION10chain 'B' and (resid 576 through 763 )
11X-RAY DIFFRACTION11chain 'B' and (resid 764 through 815 )
12X-RAY DIFFRACTION12chain 'B' and (resid 816 through 958 )
13X-RAY DIFFRACTION13chain 'B' and (resid 959 through 1016 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1017 through 1093 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 19 )
16X-RAY DIFFRACTION16chain 'C' and (resid 20 through 29 )
17X-RAY DIFFRACTION17chain 'C' and (resid 30 through 50 )
18X-RAY DIFFRACTION18chain 'C' and (resid 51 through 58 )
19X-RAY DIFFRACTION19chain 'C' and (resid 59 through 66 )
20X-RAY DIFFRACTION20chain 'C' and (resid 67 through 80 )
21X-RAY DIFFRACTION21chain 'C' and (resid 81 through 98 )
22X-RAY DIFFRACTION22chain 'C' and (resid 99 through 112 )
23X-RAY DIFFRACTION23chain 'C' and (resid 113 through 124 )
24X-RAY DIFFRACTION24chain 'C' and (resid 125 through 157 )
25X-RAY DIFFRACTION25chain 'D' and (resid 201 through 203 )

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