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- PDB-9n1s: Crystal structure of the Transport and Golgi Organization protein... -

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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 / cytoplasm / cytosol
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.36 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

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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

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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 )

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