[English] 日本語
Yorodumi
- PDB-5vnk: Crystal structure of Sec23a/Sec24a/Sec22 complexed with a C-termi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vnk
TitleCrystal structure of Sec23a/Sec24a/Sec22 complexed with a C-terminal LL sorting motif
Components
  • (Protein transport protein ...Protein targeting) x 2
  • C-terminal LL
  • 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.1Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein transport protein Sec23A
B: Protein transport protein Sec24A
C: Vesicle-trafficking protein SEC22b
D: C-terminal LL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,2096
Polymers189,0794
Non-polymers1312
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-19 kcal/mol
Surface area66520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.180, 97.615, 130.546
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
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

-
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 LL


Mass: 531.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 2 types, 61 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.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50mM HEPES PH 7.8, 0.5M NaAc and 12% PEG4K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / 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: 2.55→130.546 Å / Num. obs: 60273 / % possible obs: 99.5 % / Redundancy: 3.7 % / Net I/σ(I): 2.3

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NUT

2nut


Resolution: 2.55→130.546 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 29.31
RfactorNum. reflection% reflection
Rfree0.2514 3041 5.05 %
Rwork0.1958 --
obs0.1987 60273 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→130.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12483 0 2 59 12544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312777
X-RAY DIFFRACTIONf_angle_d0.64517309
X-RAY DIFFRACTIONf_dihedral_angle_d13.1377780
X-RAY DIFFRACTIONf_chiral_restr0.0431955
X-RAY DIFFRACTIONf_plane_restr0.0052236
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)
11.3494-0.14711.25171.76380.7291.66270.09810.24750.2485-0.1233-0.0796-0.0333-0.15230.1371-0.14320.8170.1155-0.00940.61370.12160.4242-29.717115.2852-5.1498
22.33720.83870.38312.51640.85251.3843-0.14820.2653-0.0812-0.8968-0.11380.69930.094-0.08310.19561.07540.0449-0.19780.47790.00150.5912-40.55894.1956-9.2999
31.6925-0.49720.9822.2535-1.18282.21150.1058-0.0071-0.3103-0.2299-0.0239-0.00030.03390.0751-0.07110.30820.04520.02160.3664-0.00480.3897-18.362183.051920.9551
41.591-0.30280.44472.3703-0.60222.28720.02530.20860.1011-0.0892-0.0828-0.4697-0.09430.46320.0910.33490.05160.01690.4890.04910.4308-7.345393.175522.2585
50.5387-0.18070.48582.7287-0.28191.02330.00410.32760.0535-0.6919-0.1054-0.3535-0.07850.15570.06620.59880.05950.09050.58540.10190.4148-21.475109.67143.0002
61.8888-0.6722-0.57752.90440.55343.7187-0.0599-0.29940.13260.35420.04470.5241-0.6125-0.24930.11110.63220.05820.02480.47590.03970.5355-28.5895123.220230.3694
71.311-0.95010.21752.4632-0.73891.57160.1095-0.12020.1892-0.1548-0.1997-0.4550.01490.46550.17210.627-0.0616-0.08530.56930.10560.7073-16.3731125.181518.6639
81.74830.37130.18021.0324-0.01660.8302-0.0429-0.1967-0.28810.3793-0.0111-0.37840.289-0.22660.10330.60350.09260.02660.50020.04150.470230.893130.46851.9742
93.2217-0.1025-0.17051.9479-0.42351.3921-0.1848-0.25720.37760.56220.0725-0.03850.08110.05030.20140.47530.0916-0.06050.4111-0.01860.302630.200147.824451.6605
103.4595-0.1447-0.22732.81290.32542.7334-0.0813-1.15520.88430.74710.1864-0.5194-0.61230.45720.00240.67970.055-0.13180.818-0.25130.739942.068156.82862.2316
111.6451-0.9587-0.06172.0044-0.30460.9951-0.00950.04730.125-0.056-0.07510.2924-0.1379-0.20190.09790.34720.0691-0.00430.4184-0.07440.49983.697761.887338.6778
121.6343-0.66480.19141.5578-0.06470.9131-0.01140.2293-0.0124-0.1776-0.0860.1610.03270.04580.10020.35490.03430.03860.3503-0.04780.362614.640951.894636.7602
131.5827-0.9319-0.6861.9181-0.05291.0479-0.1722-0.23590.26510.14520.2056-0.43160.07580.29980.01260.37370.0862-0.03190.429-0.06080.456234.038246.582150.323
141.5010.4372-0.30580.3291-0.1411.2287-0.03740.0362-0.2913-0.12-0.06030.04650.1372-0.06970.10520.45260.03920.05570.3567-0.07210.426214.946728.026740.7626
152.17910.4129-0.90151.0808-0.14531.20560.00040.4096-0.1853-0.2087-0.0470.06870.0703-0.38790.00790.5025-0.0110.06950.522-0.0440.50877.821926.089941.3075
162.96170.07470.27782.9154-1.4184.1015-0.00430.744-0.78580.09630.22960.2556-0.59030.03430.0220.6340.0841-0.27930.5855-0.22390.728718.921281.817555.8993
170.01620.0224-0.30170.0322-0.23285.63090.86190.022-0.1218-0.11250.12651.07460.15810.0316-0.78561.82840.33780.40191.17460.10021.926915.940778.591841.5785
184.5410.22920.46914.67351.03156.4601-0.68920.40140.3886-0.79120.1215-0.1229-0.39490.81340.68970.8351-0.034-0.09820.7172-0.04780.673827.361485.757654.956
194.176-0.36611.22565.4665-3.71742.8661-0.60670.45591.3767-0.6792-0.12080.5985-1.29450.10410.57350.91260.0576-0.2940.63170.03780.871819.226891.920152.9732
204.09790.2196-0.5445.8488-1.28345.418-0.2072-0.41091.2126-0.0575-0.13061.7259-0.3073-0.54420.59770.7050.1545-0.29570.962-0.3161.13419.935588.859359.4939
213.85650.56180.94542.9252-0.07336.78020.6094-0.8853-0.34331.2601-0.0927-0.17470.513-0.0955-0.25990.9075-0.0323-0.0930.6741-0.17960.697317.343774.520465.8659
225.4791-4.59531.99264.6934-3.9317.4208-0.59090.58860.490.24780.23330.47850.3401-0.40010.56680.72280.0928-0.21460.7675-0.11770.99826.769280.428453.4836
230.65670.26071.27860.59880.35912.327-0.47960.23860.3642-0.31340.0619-0.4135-0.8497-0.22440.30681.3840.2548-0.43711.0759-0.2021.32468.549693.886548.0836
241.571-0.99460.66691.7385-0.68090.3553-0.20370.74920.4562-1.13080.1449-0.5175-0.86450.39430.531.6213-0.2946-0.21541.27240.08881.174330.714594.402550.7909
250.012-0.03840.00410.2453-0.05020.012-0.05910.0015-0.0302-0.05140.0383-0.04910.02060.072-0.00121.24670.3465-0.40451.49110.0882.485430.696564.019849.2729
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 232 )
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 379 )
5X-RAY DIFFRACTION5chain 'A' and (resid 380 through 609 )
6X-RAY DIFFRACTION6chain 'A' and (resid 610 through 698 )
7X-RAY DIFFRACTION7chain 'A' and (resid 699 through 764 )
8X-RAY DIFFRACTION8chain 'B' and (resid 346 through 396 )
9X-RAY DIFFRACTION9chain 'B' and (resid 397 through 431 )
10X-RAY DIFFRACTION10chain 'B' and (resid 432 through 476 )
11X-RAY DIFFRACTION11chain 'B' and (resid 477 through 658 )
12X-RAY DIFFRACTION12chain 'B' and (resid 659 through 784 )
13X-RAY DIFFRACTION13chain 'B' and (resid 785 through 839 )
14X-RAY DIFFRACTION14chain 'B' and (resid 840 through 1016 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1017 through 1093 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 19 )
17X-RAY DIFFRACTION17chain 'C' and (resid 20 through 29 )
18X-RAY DIFFRACTION18chain 'C' and (resid 30 through 50 )
19X-RAY DIFFRACTION19chain 'C' and (resid 51 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 149 )
24X-RAY DIFFRACTION24chain 'C' and (resid 150 through 157 )
25X-RAY DIFFRACTION25chain 'D' and (resid 356 through 358 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more