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

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Basic information

Entry
Database: PDB / ID: 5vng
TitleCrystal structure of Sec23a/Sec24a/Sec22 complexed with a C-terminal II sorting motif
Components
  • (Protein transport protein ...Protein targeting) x 2
  • C-terminal ILE-ILE
  • Vesicle-trafficking protein SEC22b
KeywordsPROTEIN TRANSPORT / ER retention / p24 / protein trafficking / protein quality control
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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

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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 ILE-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,3386
Polymers189,2084
Non-polymers1312
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-19 kcal/mol
Surface area65270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.262, 97.102, 130.032
Angle α, β, γ (deg.)90.00, 90.19, 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
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
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 ILE-ILE


Mass: 660.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 60 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.: 58 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
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→50 Å / Num. obs: 54087 / % possible obs: 98.2 % / Redundancy: 3.2 % / Net I/σ(I): 1.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.6→48.962 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 31.08
RfactorNum. reflection% reflection
Rfree0.2571 1802 3.44 %
Rwork0.1991 --
obs0.2011 52314 91.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12349 0 2 58 12409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212614
X-RAY DIFFRACTIONf_angle_d0.53717104
X-RAY DIFFRACTIONf_dihedral_angle_d11.1147681
X-RAY DIFFRACTIONf_chiral_restr0.0411942
X-RAY DIFFRACTIONf_plane_restr0.0042209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67030.32611020.27552841X-RAY DIFFRACTION68
2.6703-2.74890.29881030.2753109X-RAY DIFFRACTION74
2.7489-2.83760.31061130.28513294X-RAY DIFFRACTION79
2.8376-2.9390.34741430.29133852X-RAY DIFFRACTION92
2.939-3.05670.32091490.27224124X-RAY DIFFRACTION98
3.0567-3.19580.33711480.2614123X-RAY DIFFRACTION99
3.1958-3.36420.30641430.23114139X-RAY DIFFRACTION98
3.3642-3.57490.27331510.22454115X-RAY DIFFRACTION98
3.5749-3.85080.27981550.19954225X-RAY DIFFRACTION99
3.8508-4.23820.23371450.17534137X-RAY DIFFRACTION98
4.2382-4.8510.21831490.16094139X-RAY DIFFRACTION98
4.851-6.10990.24231480.18064210X-RAY DIFFRACTION99
6.1099-48.97020.22231530.17214204X-RAY DIFFRACTION97
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)
12.57340.8073-0.53314.7515-0.35131.8029-0.0190.50310.0949-0.8249-0.0202-0.5007-0.1004-0.1704-0.02071.12480.15460.22370.6354-0.06590.5853183.6164-102.4536-7.5251
23.8903-1.3434-2.84632.40611.24324.28250.01450.03090.1365-0.41540.014-0.39180.08610.0967-0.14550.54410.01660.11720.4197-0.04830.5634176.5362-89.006816.3379
32.66290.1102-0.46814.08020.81192.61010.05150.22390.144-0.1234-0.12210.67910.0864-0.42180.00990.39690.09230.06590.5892-0.06650.6053155.8922-88.990522.3333
41.3232-0.0223-0.02073.25950.28041.5424-0.00060.2954-0.122-0.6711-0.07590.30340.26760.02390.08480.72540.05880.07870.5899-0.13060.5122170.4997-111.72855.7256
53.0504-0.11641.01016.52732.13366.45090.0257-0.4326-0.21470.37790.0954-0.32970.5734-0.1770.03590.6674-0.01210.25370.4903-0.01260.7633170.5605-122.709825.1781
64.1381.2063-0.95911.09910.23671.4605-0.1271-0.1440.28710.3547-0.01220.374-0.11220.16020.14690.63170.12660.11550.4832-0.02780.6706115.4854-32.552149.4607
75.22480.2706-0.32831.9614-1.14352.86290.0723-1.3291-1.19180.7021-0.02240.48850.2225-0.5569-0.08070.78980.10060.29240.80110.18590.9642112.6036-55.700362.1563
84.5023-1.4824-1.78862.70050.73332.85140.00930.0681-0.43650.0666-0.134-0.07610.26120.14830.13880.45440.11030.08690.44390.07510.6049145.6809-64.930540.3856
93.5716-0.07420.55453.0787-0.15062.259-0.02510.47170.0963-0.479-0.1686-0.44830.03780.24310.20570.43910.1090.16110.45880.01940.583142.6661-55.752130.8061
105.7133-1.3539-0.47981.13850.26120.7028-0.1218-0.1008-0.17350.24710.07670.22950.0405-0.11950.06220.51960.04750.12180.37420.04830.5582124.3857-51.837645.4091
111.6931-0.60640.29240.70170.31611.0171-0.17830.09650.115-0.1057-0.06630.0844-0.07330.03640.23570.53450.06630.07620.38330.09210.5154123.988-33.20739.5671
129.3101-0.02941.44082.84910.34474.6873-0.10160.07590.9355-0.1993-0.0995-0.3406-0.77120.53060.19050.6043-0.0650.07180.42150.04160.5936146.6832-21.599847.7843
136.0632-0.76474.06551.7598-1.13544.1927-0.13270.69070.3522-0.075-0.1659-0.163-0.41480.71850.21820.6261-0.08940.10050.54720.04790.6172139.9052-26.090941.4402
147.42-1.974-1.65038.31034.31762.3022-0.7440.8769-0.13790.54050.2108-0.69181.0179-0.650.49820.82250.01810.34810.62490.17640.8281129.1578-81.898555.7762
157.49283.9089-2.01424.90681.66295.30821.12320.38820.4506-0.2737-0.0087-0.7194-1.0387-0.1346-1.02731.4245-0.0269-0.05591.00550.37072.1184132.2493-78.634841.5322
167.36090.82161.51487.9963-3.83769.826-0.74690.37640.549-1.2665-0.46060.20250.4812-0.3091.09581.22990.03660.34080.64970.07891.1338120.7452-85.753654.6992
179.9761-0.6964-5.47172.1752-0.03963.0850.45671.1954-1.011-1.6114-0.6199-0.54340.4413-1.30340.19132.0921-0.23630.61560.6259-0.16611.3114125.1124-95.094250.708
187.5550.07590.08945.64172.55668.642-0.90730.0218-1.5709-0.8441-0.0402-1.2751.06351.15120.73881.25260.14140.59960.73810.11111.3058133.951-89.794956.3662
199.3381-1.2176.18443.35180.94669.76810.4275-0.44380.99891.3542-0.7738-0.0940.56970.27270.47331.1073-0.00530.22210.73060.29090.8355130.9218-74.627765.6152
202.0248-3.6256-3.49287.88756.38678.6841-1.00070.3693-1.0931-0.37940.1808-0.5895-0.07291.40630.52570.80970.15420.24921.08740.27521.2205141.408-80.48253.3371
211.5999-1.50520.0166.6281-0.6125.4058-1.35750.8414-2.1348-1.20190.6360.22512.4363-0.03481.00161.7319-0.07950.46291.0586-0.05611.476128.8232-94.426849.2898
223.52581.6070.41231.7704-1.12551.73070.87690.15210.4809-0.3855-0.03560.245-0.62270.206-0.651.41650.05780.36950.8903-0.34331.5413116.9144-64.606148.0465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 169 )
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 379 )
4X-RAY DIFFRACTION4chain 'A' and (resid 380 through 646 )
5X-RAY DIFFRACTION5chain 'A' and (resid 647 through 764 )
6X-RAY DIFFRACTION6chain 'B' and (resid 347 through 411 )
7X-RAY DIFFRACTION7chain 'B' and (resid 412 through 486 )
8X-RAY DIFFRACTION8chain 'B' and (resid 487 through 584 )
9X-RAY DIFFRACTION9chain 'B' and (resid 585 through 724 )
10X-RAY DIFFRACTION10chain 'B' and (resid 725 through 815 )
11X-RAY DIFFRACTION11chain 'B' and (resid 816 through 958 )
12X-RAY DIFFRACTION12chain 'B' and (resid 959 through 1016 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1017 through 1093 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 19 )
15X-RAY DIFFRACTION15chain 'C' and (resid 20 through 29 )
16X-RAY DIFFRACTION16chain 'C' and (resid 30 through 50 )
17X-RAY DIFFRACTION17chain 'C' and (resid 51 through 58 )
18X-RAY DIFFRACTION18chain 'C' and (resid 59 through 99 )
19X-RAY DIFFRACTION19chain 'C' and (resid 100 through 112 )
20X-RAY DIFFRACTION20chain 'C' and (resid 113 through 125 )
21X-RAY DIFFRACTION21chain 'C' and (resid 126 through 157 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 4 )

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