[English] 日本語
Yorodumi
- PDB-9n1s: Crystal structure of the Transport and Golgi Organization protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n1s
TitleCrystal structure of the Transport and Golgi Organization protein 2 Homolog (TANGO2) tetragonal form
ComponentsTransport and Golgi organization protein 2 homolog
KeywordsLIPID TRANSPORT / TANGO2 / TANGO2-related disease
Function / homology
Function and homology information


Golgi organization / protein secretion / Golgi apparatus / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Transport and Golgi organisation protein 2 / Transport and Golgi organisation 2
Similarity search - Domain/homology
PHOSPHATE ION / Transport and Golgi organization protein 2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLovell, S. / Cooper, A. / Powers, A. / Battaile, K.P. / Moshen, A.W. / Ghaloul-Gonzalez, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: Proteins / Year: 2025
Title: The Crystal Structure of Human Transport and Golgi Organization 2 Homolog (TANGO2) Protein Reveals an alpha beta beta alpha-Fold Arrangement.
Authors: Cooper, A. / Powers, A. / Battaile, K.P. / Mohsen, A.W. / Johnson, D.K. / Lovell, S. / Ghaloul-Gonzalez, L.
History
DepositionJan 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transport and Golgi organization protein 2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9753
Polymers31,8451
Non-polymers1302
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.895, 49.895, 241.716
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Transport and Golgi organization protein 2 homolog


Mass: 31844.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TANGO2, C22orf25 / Plasmid: pET-27b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6ICL3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Berkeley Screen B8: 20% (w/v) PEG 3350, 70 mM Bis-Tris Propane, 30 mM Citric Acid pH 7.6 , TANGO2 at 5.5 mg/mL. Plate 19608 well B8 drop 1, Puck: PSL-2010, Cryo: 80% (v/v) crystallant and 20% (v/v) PEG 200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 14, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→46.12 Å / Num. obs: 14036 / % possible obs: 96.4 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.046 / Rrim(I) all: 0.113 / Χ2: 0.99 / Net I/σ(I): 10.8 / Num. measured all: 82398
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 1.066 / Num. measured all: 8441 / Num. unique obs: 1399 / CC1/2: 0.781 / Rpim(I) all: 0.468 / Rrim(I) all: 1.167 / Χ2: 1.05 / Net I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
PHENIX(dev_5533: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.12 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 690 4.94 %
Rwork0.2051 --
obs0.2072 13964 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 6 56 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042196
X-RAY DIFFRACTIONf_angle_d0.5752988
X-RAY DIFFRACTIONf_dihedral_angle_d15.624795
X-RAY DIFFRACTIONf_chiral_restr0.045331
X-RAY DIFFRACTIONf_plane_restr0.005386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.3361450.2912652X-RAY DIFFRACTION100
2.48-2.730.34421340.26792419X-RAY DIFFRACTION90
2.73-3.120.2751400.23882721X-RAY DIFFRACTION100
3.12-3.930.25471210.19642542X-RAY DIFFRACTION92
3.93-46.120.20321500.1772940X-RAY DIFFRACTION99
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)
13.5735-2.6174-1.13443.59130.78654.099-0.035-0.26130.0710.2650.00780.22220.0764-0.1736-0.0090.4257-0.15140.00210.4516-0.05110.4139-25.5513-7.933-11.1408
24.4498-0.6627-0.12593.04721.60456.1083-0.0485-0.45450.5672-0.3380.3285-0.5118-0.57161.031-0.28790.4702-0.18460.03850.5894-0.05390.4427-8.37951.002-8.9489
34.21240.84990.60311.8103-0.61943.48750.286-0.36040.2239-0.2467-0.1756-0.3795-0.6450.7405-0.11150.3861-0.08790.04810.4822-0.03680.4623-12.34561.4593-14.8076
42.73231.09041.45153.4295-0.22331.3340.23770.3270.3755-0.4972-0.3434-0.7997-0.29980.19520.0070.5454-0.08650.00390.55280.07740.6272-13.59023.3784-24.4685
53.5443-0.1575-0.33592.77310.02922.6079-0.00760.18930.3049-0.098-0.0213-0.025-0.1584-0.03010.01440.3941-0.06850.01580.3402-0.03570.3891-24.92830.7256-23.1402
66.0675-2.8743-3.80045.16531.7162.3826-0.143-0.4538-0.93990.1959-0.58591.12810.7758-0.12720.6060.455-0.16510.04960.4812-0.0170.5111-26.2942-19.626-15.4998
75.10480.4836-3.71213.94510.56122.9286-0.3515-0.4111-0.24060.2711-0.34390.1649-0.12920.12840.7240.3919-0.0846-0.02020.64470.04810.4166-22.6319-16.7697-3.9516
82.2542-0.3008-0.56562.21320.78962.67240.20110.116-0.40160.13260.0304-0.1243-0.0303-0.0473-0.18570.4339-0.0452-0.00430.5262-0.02950.4471-12.7607-18.7478-26.6447
94.2782-0.08281.6842.7794-1.13462.61490.1943-0.4096-0.24920.0644-0.23840.0886-0.07110.1278-0.02690.4985-0.19460.00790.6367-0.04920.3411-14.0215-8.3852-5.0045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 164 )
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 181 )
7X-RAY DIFFRACTION7chain 'A' and (resid 182 through 197 )
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 237 )
9X-RAY DIFFRACTION9chain 'A' and (resid 238 through 275 )

+
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