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

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Basic information

Entry
Database: PDB / ID: 5vnf
TitleCrystal structure of Sec23a/Sec24a/Sec22 complexed with a C-terminal VV sorting motif
Components
  • (Protein transport protein ...Protein targeting) x 2
  • C-terminal VV Sorting motif: VAL-THR-SER-VAL-VAL
  • 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 / COPII-coated vesicle cargo loading / COPI-dependent Golgi-to-ER retrograde traffic / COPII vesicle coat / SNARE complex / negative regulation of autophagosome assembly ...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 / SNARE complex / negative regulation of autophagosome assembly / 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 / protein transport / synaptic vesicle / 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: 2.407 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
DepositionApr 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 VV Sorting motif: VAL-THR-SER-VAL-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,1816
Polymers189,0504
Non-polymers1312
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-15 kcal/mol
Surface area66230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.824, 97.077, 129.820
Angle α, β, γ (deg.)90.00, 90.12, 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 C-terminal VV Sorting motif: VAL-THR-SER-VAL-VAL


Mass: 503.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: C-terminal VV sorting motif / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 109 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.: 107 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
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: 2.4→48.822 Å / Num. obs: 66635 / % possible obs: 99 % / Redundancy: 3.1 % / Net I/σ(I): 1.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.407→48.822 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.1
RfactorNum. reflection% reflection
Rfree0.2412 2006 3.01 %
Rwork0.2045 --
obs0.2055 66635 93.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.407→48.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12476 0 2 107 12585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312778
X-RAY DIFFRACTIONf_angle_d0.61417322
X-RAY DIFFRACTIONf_dihedral_angle_d11.7967785
X-RAY DIFFRACTIONf_chiral_restr0.0441957
X-RAY DIFFRACTIONf_plane_restr0.0042238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4067-2.46690.3317960.31752942X-RAY DIFFRACTION60
2.4669-2.53360.37741150.29623764X-RAY DIFFRACTION77
2.5336-2.60810.31121410.27794339X-RAY DIFFRACTION88
2.6081-2.69230.28781450.26584665X-RAY DIFFRACTION95
2.6923-2.78850.2941430.26614791X-RAY DIFFRACTION98
2.7885-2.90020.3411500.27494858X-RAY DIFFRACTION99
2.9002-3.03220.31441500.25964900X-RAY DIFFRACTION99
3.0322-3.1920.33051560.24634869X-RAY DIFFRACTION99
3.192-3.39190.24871470.23524918X-RAY DIFFRACTION99
3.3919-3.65370.24321510.21894865X-RAY DIFFRACTION99
3.6537-4.02130.23451540.19684920X-RAY DIFFRACTION99
4.0213-4.60280.21881470.16344851X-RAY DIFFRACTION98
4.6028-5.79750.21731560.17364964X-RAY DIFFRACTION99
5.7975-48.83240.17461550.16514983X-RAY DIFFRACTION99
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)
12.0490.879-0.43995.3422-0.841.1545-0.05230.42440.1041-0.9366-0.0887-0.4558-0.0251-0.14890.14360.93110.10680.13570.6272-0.0580.484184.1506-101.2054122.0091
23.1399-1.0399-1.19442.76711.15472.49030.1520.19390.4292-0.3798-0.0153-0.0391-0.1667-0.2113-0.15680.3380.0347-0.00070.4054-0.00740.3885165.7623-82.5496150.6308
32.5628-0.1433-0.87573.69850.4862.81280.00350.3615-0.1341-0.1528-0.06320.71840.1643-0.56370.05640.32140.0564-0.01150.5759-0.07520.4894154.8148-92.6769151.9782
41.4757-0.2211-0.02093.66530.0922.12130.10680.5366-0.0593-1.1082-0.10180.29210.0195-0.1929-0.01840.62420.0889-0.01630.684-0.09020.4206170.6698-104.7873130.9012
52.2426-0.2894-0.29554.0660.46012.0156-0.0054-0.1513-0.32420.0405-0.0671-0.00810.45060.02910.06710.5001-0.01780.10860.4121-0.08790.5177169.5669-122.7557150.9706
63.61972.6012-1.62162.0941-1.45342.9915-0.0838-0.24450.4440.08550.05530.568-0.1450.08530.06980.62910.11640.04810.5839-0.09730.7212118.1656-27.9749182.6712
74.9137-0.44330.27842.3155-0.12862.7665-0.0541-0.4894-0.67910.460.01010.40270.1386-0.29870.02520.41020.0490.07890.4463-0.0030.4279112.3298-48.7496184.0902
84.1084-1.2148-0.95271.67340.11171.5729-0.154-0.2073-0.24290.22420.0670.00140.21220.10410.12270.39960.02430.00810.36970.07880.4429136.8993-61.5565175.9377
92.94980.3097-0.10923.2820.17441.98190.04850.2967-0.0036-0.3666-0.1904-0.45850.0470.26180.15820.35890.06930.0840.45970.01340.4532141.89-58.0762160.4085
103.1145-1.5122-1.521.43770.511.4486-0.05590.28970.19610.0898-0.0233-0.0962-0.01980.0020.08330.32970.0092-0.03520.31110.06510.3628132.4015-50.5672171.0379
114.2216-3.63071.08535.4283-0.57741.5434-0.3014-0.4789-0.32620.38920.30370.42420.0436-0.33560.01560.35070.03780.07390.41740.06850.4304113.5324-46.2839179.8351
122.03290.39850.66970.40140.35931.3683-0.08620.11180.3811-0.1416-0.0349-0.0349-0.24640.12710.12710.4580.0188-0.00880.40240.09720.4622132.5189-27.7308170.3607
135.88320.22133.07351.5503-0.54433.3027-0.14830.68580.4084-0.3032-0.0611-0.081-0.33140.52370.1780.5184-0.0484-0.02730.44110.01780.4952139.5344-25.7469170.9108
145.3585-2.7695-2.5594.99344.29053.7410.27790.93490.4531-0.87770.0383-0.4760.5086-0.2143-0.10921.01930.10770.34990.66860.28720.8561130.6041-83.6212181.7177
151.3018-0.2620.33233.00122.31692.15850.07020.89620.1905-0.26620.06710.2943-0.1549-0.3497-0.13930.63140.04910.15830.64520.16330.7552128.3705-78.5013182.0458
166.09881.21390.527.0812-4.22532.7765-0.3921.40290.1103-1.7812-0.016-0.0124-0.1967-0.32150.31031.13130.05070.1380.70820.11750.7868120.256-82.5777180.0956
178.55872.7648-2.43917.7205-5.6574.1932-0.7071-1.2619-0.5689-0.6567-0.1028-0.38471.26890.55820.8940.75130.01620.27870.69120.13140.8427119.8972-91.4413194.1805
183.7398-0.67920.35178.4855-6.3546.9960.14610.5392-1.53310.21610.16760.33341.3062-0.4741-0.33461.2857-0.16840.28810.8141-0.18181.4199124.5481-95.056180.4527
192.9468-1.8971-2.81877.82783.96296.6287-0.50590.7878-1.3266-1.4044-0.1402-0.91661.32320.13170.65521.0740.02160.41760.6841-0.02580.952129.417-90.2196183.1233
205.7514-2.3097-2.36197.06824.5057.7162-0.5686-0.9057-1.51990.0109-0.1084-1.78050.77640.98910.45070.83740.21330.3580.95820.39191.2411137.4221-88.3588189.0653
217.11941.1127-0.55583.33962.61192.35130.56-1.00980.7920.517-0.6496-0.7302-0.0020.22040.07450.8996-0.04240.10070.75660.28680.8022129.9974-74.1158195.3405
222.7347-4.8286-2.99748.7865.46223.3991-0.78660.5774-1.0746-0.15030.0888-0.43680.1340.80290.8160.7380.10940.24270.94260.15361.0496140.6116-79.9042183.1066
233.92570.4767-2.6280.2501-0.12951.9035-1.20830.9938-1.2061-0.68180.6441-0.40331.3084-0.19650.5521.3928-0.08210.53571.03030.06631.4415127.9824-93.6614178.9535
244.86951.9682-0.19635.7646-5.12655.132-0.2626-0.28080.65430.02510.07730.98821.4528-0.18450.19590.88750.10310.17280.8460.04111.0002116.7245-64.4288176.1767
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 232 )
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 379 )
4X-RAY DIFFRACTION4chain 'A' and (resid 380 through 557 )
5X-RAY DIFFRACTION5chain 'A' and (resid 558 through 764 )
6X-RAY DIFFRACTION6chain 'B' and (resid 346 through 385 )
7X-RAY DIFFRACTION7chain 'B' and (resid 386 through 451 )
8X-RAY DIFFRACTION8chain 'B' and (resid 452 through 575 )
9X-RAY DIFFRACTION9chain 'B' and (resid 576 through 707 )
10X-RAY DIFFRACTION10chain 'B' and (resid 708 through 784 )
11X-RAY DIFFRACTION11chain 'B' and (resid 785 through 839 )
12X-RAY DIFFRACTION12chain 'B' and (resid 840 through 1016 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1017 through 1093 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 9 )
15X-RAY DIFFRACTION15chain 'C' and (resid 10 through 29 )
16X-RAY DIFFRACTION16chain 'C' and (resid 30 through 43 )
17X-RAY DIFFRACTION17chain 'C' and (resid 44 through 50 )
18X-RAY DIFFRACTION18chain 'C' and (resid 51 through 58 )
19X-RAY DIFFRACTION19chain 'C' and (resid 59 through 80 )
20X-RAY DIFFRACTION20chain 'C' and (resid 81 through 99 )
21X-RAY DIFFRACTION21chain 'C' and (resid 100 through 112 )
22X-RAY DIFFRACTION22chain 'C' and (resid 113 through 125 )
23X-RAY DIFFRACTION23chain 'C' and (resid 126 through 157 )
24X-RAY DIFFRACTION24chain 'D' and (resid 7 through 11 )

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