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- PDB-5vnn: Crystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylb... -

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Basic information

Entry
Database: PDB / ID: 5vnn
TitleCrystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylbutyric acid (50mM soaking)
Components
  • (Protein transport protein ...Protein targeting) x 2
  • 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 / vesicle fusion with Golgi apparatus / 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 / SNARE complex ...Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / 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 / SNARE complex / SNAP receptor activity / Cargo concentration in the ER / Regulation of cholesterol biosynthesis by SREBP (SREBF) / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-mediated vesicle transport / ER-Phagosome pathway / syntaxin binding / endoplasmic reticulum to Golgi vesicle-mediated transport / extrinsic component of membrane / endoplasmic reticulum exit site / SNARE binding / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / cholesterol homeostasis / vesicle-mediated transport / protein localization to plasma membrane / intracellular protein transport / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of protein secretion / ER to Golgi transport vesicle membrane / positive regulation of protein catabolic process / melanosome / protein transport / synaptic vesicle / endoplasmic reticulum-Golgi intermediate compartment / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / zinc ion binding / membrane => GO:0016020 / cytosol
Similarity search - Function
Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Longin domain / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Sec23, C-terminal / Protein transport protein Sec23 ...Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Longin domain / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Sec23, C-terminal / Protein transport protein Sec23 / Sec24-like, 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 / Zinc finger, Sec23/Sec24-type / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Zn-finger domain of Sec23/24 / Sec23/Sec24 beta-sandwich domain / Sec23/Sec24, trunk domain / Synaptobrevin-like / Synaptobrevin / Gelsolin-like domain superfamily / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Severin / Gelsolin-like domain / Gelsolin repeat / Severin / Longin-like domain superfamily / von Willebrand factor, type A domain / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor A-like domain superfamily / Beta-Lactamase / 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
Protein transport protein Sec24A / 4-PHENYL-BUTANOIC ACID / Vesicle-trafficking protein SEC22b / Protein transport protein Sec23A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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

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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)188,8426
Polymers188,5473
Non-polymers2953
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.016, 97.715, 128.967
Angle α, β, γ (deg.)90.00, 89.59, 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
Production host: Insect cell expression vector pTIE1 (unknown)
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
Production host: Insect cell expression vector pTIE1 (unknown)
References: UniProt: O95486

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Protein , 1 types, 1 molecules C

#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

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Non-polymers , 3 types, 47 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CLT / 4-PHENYL-BUTANOIC ACID / GAMMA-PHENYL-BUTYRIC ACID


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.5→48.858 Å / Num. obs: 53119 / % possible obs: 99.2 % / Redundancy: 3 % / Net I/σ(I): 13.3

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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
Resolution: 2.501→48.858 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 33.08
RfactorNum. reflection% reflection
Rfree0.2505 2007 3.78 %
Rwork0.2099 --
obs0.2115 53119 83.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→48.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12415 0 14 44 12473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212709
X-RAY DIFFRACTIONf_angle_d0.55917215
X-RAY DIFFRACTIONf_dihedral_angle_d12.5097740
X-RAY DIFFRACTIONf_chiral_restr0.0411946
X-RAY DIFFRACTIONf_plane_restr0.0042225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5012-2.56370.409720.30681797X-RAY DIFFRACTION42
2.5637-2.63310.3876870.30942157X-RAY DIFFRACTION49
2.6331-2.71050.29091050.29472489X-RAY DIFFRACTION57
2.7105-2.7980.36221120.2992884X-RAY DIFFRACTION66
2.798-2.8980.33741250.30353302X-RAY DIFFRACTION76
2.898-3.0140.36791590.28593883X-RAY DIFFRACTION90
3.014-3.15120.33031670.27714315X-RAY DIFFRACTION98
3.1512-3.31730.28571670.24754315X-RAY DIFFRACTION99
3.3173-3.52510.25951730.23754302X-RAY DIFFRACTION99
3.5251-3.79710.28161660.21114270X-RAY DIFFRACTION98
3.7971-4.17910.23461670.18764353X-RAY DIFFRACTION99
4.1791-4.78330.19761680.16484304X-RAY DIFFRACTION98
4.7833-6.02470.23691720.1834373X-RAY DIFFRACTION99
6.0247-48.86680.18731670.17484368X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.97281.2105-0.76893.1255-0.5881.4542-0.03960.19220.1419-0.34540.0333-0.3991-0.24580.1275-0.02910.77490.00260.25110.3549-0.0480.556636.7102-101.3323-7.8413
21.9863-0.2447-0.2852.34090.65451.18660.04530.04420.1574-0.1044-0.06110.31440.0028-0.1869-0.01670.39070.03440.14840.27710.00940.467912.4716-88.522621.3818
31.12760.0166-0.2262.19120.65321.2561-0.05590.2155-0.0584-0.55280.00260.12030.025-0.0143-0.00730.63330.0280.16940.3764-0.02560.506821.6896-109.4162.6391
41.76860.09040.55512.89490.65763.58660.0835-0.3126-0.30930.415-0.0365-0.21730.5919-0.06580.0710.78050.04060.36510.41880.03540.862423.8844-122.68223.5647
52.12460.9409-0.7040.4829-0.54731.15670.0277-0.06760.09190.13410.04350.2111-0.12170.0974-0.06210.69110.07510.28430.4846-0.090.6479-30.4484-30.622951.3016
63.2351-0.56560.59121.07560.25611.8554-0.1609-0.6803-0.8458-0.02680.25640.28770.6678-0.1718-0.10230.52110.07270.30680.56450.12150.702-34.2824-51.23755.1349
72.2502-1.17050.18792.0761-0.2171.20590.0072-0.03-0.1126-0.2238-0.052-0.12460.22810.06990.07550.40410.00790.19610.27250.01930.56-7.8346-60.18938.1524
81.6733-1.04650.29941.5762-0.24010.5544-0.1125-0.0817-0.23010.07160.03890.0529-0.0135-0.07760.06310.45740.02750.18780.3037-0.01650.4612-23.9823-45.720641.6517
90.98280.19160.61580.3130.20231.8807-0.0717-0.01850.292-0.0994-0.0537-0.0798-0.20230.13280.08890.55850.01050.21550.34190.0390.6235-10.035-26.651742.7184
102.0719-0.31031.3570.1971-0.79152.107-0.0170.1410.3005-0.12-0.1915-0.1157-0.11940.33630.15390.64250.04760.16560.4255-0.02280.6521-7.5135-26.234140.7802
113.0383-0.2091-0.16875.07762.67526.22650.12660.25540.9228-0.58540.46080.1345-0.30990.0123-0.48930.78250.00980.44170.48640.21910.7613-18.5362-81.808955.2478
120.1654-0.0773-1.08190.30420.69037.15080.4790.3601-0.1303-1.087-0.0748-0.5767-0.76520.3078-0.27711.60160.15870.0421.0568-0.13411.5536-15.8721-78.504440.8646
133.1427-0.1992-0.67416.61342.39637.32070.02070.2509-0.7602-0.0915-0.37320.1551-0.1765-0.95730.18930.7643-0.08810.40830.75050.05621.0601-26.0564-88.15453.3198
147.1805-0.69732.33377.18821.75222.7449-0.47920.6322-1.2633-0.9890.2814-0.3740.59990.31640.08690.9425-0.03070.4620.4741-0.04240.8872-17.7591-90.725252.9269
154.62740.8284-0.06195.37512.1144.34830.1373-0.1646-0.91170.1547-0.4449-0.9945-0.16850.15320.12820.88470.01050.43570.84390.26061.1767-9.6437-88.854958.6472
165.1196-0.34580.1433.0675-0.82953.45740.1517-0.32120.79820.9293-0.4487-0.0863-0.9885-0.0799-0.23391.0298-0.03510.46790.81490.31020.9734-16.9155-74.546465.1191
173.3979-2.2191-1.7964.20511.88324.1995-0.57260.6214-0.1162-0.45710.0581-0.78110.18250.26050.28390.75260.0740.41150.78380.14460.9553-6.8676-79.702753.0849
181.6179-0.31680.01181.95770.46882.2537-0.84040.7478-0.5219-0.24130.0481-0.41161.1345-0.07640.45261.1324-0.0330.56110.88390.12271.1306-16.0556-94.065248.5002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 107 )
2X-RAY DIFFRACTION2chain 'A' and (resid 108 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 396 )
6X-RAY DIFFRACTION6chain 'B' and (resid 397 through 451 )
7X-RAY DIFFRACTION7chain 'B' and (resid 452 through 707 )
8X-RAY DIFFRACTION8chain 'B' and (resid 708 through 881 )
9X-RAY DIFFRACTION9chain 'B' and (resid 882 through 1016 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1017 through 1093 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 19 )
12X-RAY DIFFRACTION12chain 'C' and (resid 20 through 29 )
13X-RAY DIFFRACTION13chain 'C' and (resid 30 through 58 )
14X-RAY DIFFRACTION14chain 'C' and (resid 59 through 80 )
15X-RAY DIFFRACTION15chain 'C' and (resid 81 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 100 through 112 )
17X-RAY DIFFRACTION17chain 'C' and (resid 113 through 124 )
18X-RAY DIFFRACTION18chain 'C' and (resid 125 through 157 )

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