[English] 日本語
Yorodumi
- PDB-2nut: Crystal Structure of the human Sec23a/24a heterodimer, complexed ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nut
TitleCrystal Structure of the human Sec23a/24a heterodimer, complexed with the SNARE protein Sec22b
Components
  • Protein transport protein Sec23A
  • Protein transport protein Sec24A
  • Vesicle-trafficking protein SEC22b
KeywordsPROTEIN TRANSPORT / Human COPII Sec23-24 complexed with Sec22
Function / homology
Function and homology information


regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPII vesicle coat / 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 / COPI-dependent Golgi-to-ER retrograde traffic ...regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPII vesicle coat / 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 / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / GTPase activator activity / cholesterol homeostasis / SNARE binding / positive regulation of protein secretion / protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / phagocytic vesicle membrane / positive regulation of protein catabolic process / melanosome / protein transport / ER-Phagosome pathway / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / 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 / Gelsolin-like domain superfamily / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / Longin-like domain superfamily / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor, type A domain / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMancias, J.D. / Goldberg, J.
CitationJournal: Mol.Cell / Year: 2007
Title: The Transport Signal on Sec22 for Packaging into COPII-Coated Vesicles is a Conformational Epitope
Authors: Mancias, J.D. / Goldberg, J.
History
DepositionNov 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,0615
Polymers193,9303
Non-polymers1312
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-15 kcal/mol
Surface area66150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.280, 97.580, 129.800
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Protein transport protein Sec23A / SEC23-related protein A


Mass: 86551.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A / Production host: Hi5 insect cells / References: UniProt: Q15436
#2: Protein Protein transport protein Sec24A / SEC24-related protein A


Mass: 84961.578 Da / Num. of mol.: 1 / Fragment: Sec24a fragment lacking n-terminal residues 1-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24A / Production host: Hi5 insect cells / References: UniProt: O95486
#3: Protein Vesicle-trafficking protein SEC22b / SEC22 vesicle-trafficking protein homolog B / SEC22 vesicle-trafficking protein-like 1 / ERS24 / ERS- 24


Mass: 22416.590 Da / Num. of mol.: 1 / Fragment: Sec22b cytosolic domain, residues 1-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC22B, SEC22L1 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / References: UniProt: O75396
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 10% (w/v) PEG 4000, 0.5M sodium acetate and 50 mM Tris buffer, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2005
Details: Mirror: Platinum-coated 1:1 focusing toroidal mirror
RadiationMonochromator: Double silicon crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 77749 / % possible obs: 94.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.061 / Χ2: 1.43 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.1 / Num. unique all: 7880 / Rsym value: 0.268 / Χ2: 1.098 / % possible all: 96.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NUP

2nup


Resolution: 2.3→30 Å / FOM work R set: 0.795 / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3747 4.6 %RANDOM
Rwork0.219 ---
obs-73609 89.5 %-
Solvent computationBsol: 43.746 Å2
Displacement parametersBiso mean: 47.504 Å2
Baniso -1Baniso -2Baniso -3
1-0.208 Å20 Å27.691 Å2
2--2.452 Å20 Å2
3----2.659 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12475 0 2 301 12778
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.385
X-RAY DIFFRACTIONc_mcbond_it3.7223.5
X-RAY DIFFRACTIONc_scbond_it5.144
X-RAY DIFFRACTIONc_mcangle_it5.2554
X-RAY DIFFRACTIONc_scangle_it6.7284.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.320.325840.3112841368
2.32-2.330.424650.31512771342
2.33-2.350.361590.31313151374
2.35-2.360.393680.31512171285
2.36-2.380.379680.29213661434
2.38-2.40.315600.28713281388
2.4-2.420.353560.30213101366
2.42-2.440.379750.28713271402
2.44-2.460.354650.28913841449
2.46-2.480.374680.30613491417
2.48-2.50.339590.27514231482
2.5-2.520.324770.2713751452
2.52-2.540.299830.27313941477
2.54-2.570.373670.28213631430
2.57-2.590.308820.27514161498
2.59-2.620.312790.26414231502
2.62-2.640.3750.26613631438
2.64-2.670.398860.29214011487
2.67-2.70.289700.25513941464
2.7-2.730.359620.26714011463
2.73-2.760.341840.26614301514
2.76-2.790.297550.27414221477
2.79-2.820.336750.26414261501
2.82-2.860.361820.27214891571
2.86-2.90.32730.25113891462
2.9-2.940.313900.23514091499
2.94-2.980.329760.24114701546
2.98-3.020.297830.23914251508
3.02-3.070.304880.23114651553
3.07-3.120.32680.24514601528
3.12-3.170.289850.22414911576
3.17-3.230.266920.21514461538
3.23-3.290.251760.20414761552
3.29-3.360.287790.21614761555
3.36-3.430.263790.21214731552
3.43-3.510.254780.21614531531
3.51-3.60.2721100.20414751585
3.6-3.70.236810.20514581539
3.7-3.810.232830.19914391522
3.81-3.930.217900.18314571547
3.93-4.070.183720.16714431515
4.07-4.230.188780.16414651543
4.23-4.430.196730.16114181491
4.43-4.660.234770.16914271504
4.66-4.950.195920.17313961488
4.95-5.330.296760.19914171493
5.33-5.860.24670.21914481515
5.86-6.70.258610.20414151476
6.7-8.410.237740.19213901464
8.41-300.253420.219904946
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5zinc.parzinc.top

+
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