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- PDB-7yh2: TRAPPC3 from Thorarchaeota AB25 -

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Basic information

Entry
Database: PDB / ID: 7yh2
TitleTRAPPC3 from Thorarchaeota AB25
ComponentsTRAPPC3 from Thorarchaeota AB25
KeywordsUNKNOWN FUNCTION / Asgard archaea / TRAPP
Function / homologyTrafficking protein particle complex subunit 3 / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / 2-Layer Sandwich / metal ion binding / Alpha Beta / Metanogen output domain-containing protein
Function and homology information
Biological speciesCandidatus Thorarchaeota archaeon AB_25 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsRobinson, R.C. / Tran, L.T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00476 Japan
Other privateMoore and Simons foundations GBMF9743
CitationJournal: Commun Biol / Year: 2024
Title: The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea.
Authors: Tran, L.T. / Akil, C. / Senju, Y. / Robinson, R.C.
History
DepositionJul 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jan 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAPPC3 from Thorarchaeota AB25
B: TRAPPC3 from Thorarchaeota AB25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3904
Polymers36,2592
Non-polymers1312
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-20 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.311, 68.502, 72.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRAPPC3 from Thorarchaeota AB25


Mass: 18129.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Thorarchaeota archaeon AB_25 (archaea)
Strain: AB_25 / Gene: ThorAB25_09740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9P883
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5 250 mM Mg(HCO2)2 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1.158 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.158 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 25147 / % possible obs: 99.7 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.034 / Rrim(I) all: 0.117 / Net I/σ(I): 58
Reflection shellResolution: 1.91→1.94 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 2433 / CC1/2: 0.968 / Rpim(I) all: 0.162 / Rrim(I) all: 0.457 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→32.1 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 1999 7.95 %
Rwork0.169 23148 -
obs0.1723 25147 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.31 Å2 / Biso mean: 36.106 Å2 / Biso min: 13 Å2
Refinement stepCycle: final / Resolution: 1.91→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 2 160 2662
Biso mean--26.11 42.19 -
Num. residues----312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.950.24411330.19161496162992
1.95-2.010.25961360.182116381774100
2.01-2.070.23231490.181316311780100
2.07-2.130.2371320.172316391771100
2.13-2.210.2131500.168516401790100
2.21-2.30.23281290.16216531782100
2.3-2.40.21581450.160216441789100
2.4-2.530.18721460.158316481794100
2.53-2.690.2241440.162816591803100
2.69-2.890.21781450.168916551800100
2.89-3.180.22251480.17916641812100
3.18-3.640.21721430.160716801823100
3.64-4.590.16961520.15517091861100
4.59-32.10.21941470.184617921939100
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)
13.8231-1.40980.78110.6314-0.43842.971-0.0295-0.22760.04270.09920.0835-0.00170.1899-0.05070.02090.1718-0.0036-0.0170.1548-0.01210.15624.501838.313169.3168
21.07930.6503-0.48020.94520.28391.68130.2525-0.05390.4415-0.05330.0123-0.2298-0.0920.27020.00350.1959-0.00320.01020.209-0.03540.181629.399642.934157.7433
30.74770.5488-0.52390.6961-0.20170.4820.19950.4747-0.1668-0.20290.4036-0.12770.7780.24910.01540.45220.1557-0.06150.4842-0.08480.420137.76729.502946.8111
40.85770.5564-0.1820.84490.2320.28650.10060.4941-0.5776-0.137-0.02350.17680.6821-0.32840.00860.37060.0245-0.05770.2633-0.08340.291828.504827.378647.6977
52.14030.66080.17012.1009-0.44962.11250.05470.1619-0.2526-0.0288-0.04560.07780.5532-0.2573-0.03430.264-0.0204-0.02670.2276-0.01510.219317.704731.829955.7125
65.2811-0.9344-0.84551.34270.57411.84450.3980.38770.2971-0.3174-0.042-0.1011-0.1346-0.01460.13960.19230.03710.00330.2049-0.04190.161226.657138.807750.4894
71.7584-0.7569-0.27082.13880.80362.38030.20790.21840.1371-0.07150.06970.1698-0.0549-0.77960.04520.2114-0.02-0.01760.2186-0.00550.168316.971835.227353.6266
82.98821.39171.04971.0531-0.43372.7522-0.0070.10240.0627-0.1617-0.0534-0.0913-0.07620.2006-0.00030.17540.0109-0.01580.1625-0.00870.176838.358939.054767.7984
91.1797-0.4479-0.1480.75050.53341.29520.342-0.61640.25890.3079-0.28090.2053-0.084-0.1972-0.00230.2064-0.0373-0.01440.25780.00740.201732.953339.493179.9669
100.8763-0.6851-0.28310.8508-0.08310.9036-0.0318-0.3251-0.11720.2386-0.2752-0.19930.45070.1507-0.00420.3171-0.0177-0.04670.41070.06820.461431.801422.582186.9613
110.60080.0319-0.56930.5722-0.24150.58650.3516-1.1885-0.98980.52650.0198-0.68480.0602-0.13370.00820.49360.0238-0.15920.75650.09490.671644.703623.095687.425
121.4926-0.29360.77681.30530.06551.05890.13550.0502-0.4211-0.1334-0.1448-0.57370.16410.43130.01290.21610.0202-0.02720.31210.01770.335646.174733.578674.6789
133.84412.1108-1.59491.455-1.25411.08880.2689-0.44990.04850.3779-0.07260.0593-0.3092-0.0080.07120.2195-0.0438-0.01520.26280.06570.24833.163433.478884.9389
141.50081.04150.68092.6121-0.9031.3130.3689-0.4467-0.21370.205-0.401-0.2294-0.50330.34760.00960.2422-0.0598-0.10180.38740.06420.284444.141533.366684.2948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )A2 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 47 )A27 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 61 )A48 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 77 )A62 - 77
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 117 )A78 - 117
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 141 )A118 - 141
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 157 )A142 - 157
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 26 )B2 - 26
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 48 )B27 - 48
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 77 )B49 - 77
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 91 )B78 - 91
12X-RAY DIFFRACTION12chain 'B' and (resid 92 through 117 )B92 - 117
13X-RAY DIFFRACTION13chain 'B' and (resid 118 through 131 )B118 - 131
14X-RAY DIFFRACTION14chain 'B' and (resid 132 through 157 )B132 - 157

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