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- PDB-7yh3: TRAPPC3 from Thorarchaeota SMTZ1-45 -

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Basic information

Entry
Database: PDB / ID: 7yh3
TitleTRAPPC3 from Thorarchaeota SMTZ1-45
ComponentsTRAPPC3 from Thorarchaeota SMTZ1-45
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 / 4-vinyl reductase 4VR domain-containing protein
Function and homology information
Biological speciesCandidatus Thorarchaeota archaeon SMTZ1-45 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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 SMTZ1-45
B: TRAPPC3 from Thorarchaeota SMTZ1-45
C: TRAPPC3 from Thorarchaeota SMTZ1-45
D: TRAPPC3 from Thorarchaeota SMTZ1-45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6208
Polymers72,3594
Non-polymers2624
Water12,791710
1
A: TRAPPC3 from Thorarchaeota SMTZ1-45
C: TRAPPC3 from Thorarchaeota SMTZ1-45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3104
Polymers36,1792
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area15200 Å2
MethodPISA
2
B: TRAPPC3 from Thorarchaeota SMTZ1-45
D: TRAPPC3 from Thorarchaeota SMTZ1-45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3104
Polymers36,1792
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-20 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.387, 62.060, 69.324
Angle α, β, γ (deg.)90.000, 100.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TRAPPC3 from Thorarchaeota SMTZ1-45


Mass: 18089.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea)
Gene: AM325_04720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A135VRB8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 00 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 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 51122 / % possible obs: 94.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.028 / Rrim(I) all: 0.056 / Net I/σ(I): 22.9
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2550 / CC1/2: 0.932 / Rpim(I) all: 0.177 / Rrim(I) all: 0.351

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YH2

7yh2


Resolution: 1.7→19.48 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 2486 4.86 %
Rwork0.2164 48636 -
obs0.2185 51122 81.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.8 Å2 / Biso mean: 26.2237 Å2 / Biso min: 4.02 Å2
Refinement stepCycle: final / Resolution: 1.7→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 4 710 5642
Biso mean--11.5 33.79 -
Num. residues----616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.730.3614760.29091270134639
1.73-1.770.3203750.27961469154445
1.77-1.810.2876800.26821658173850
1.81-1.850.3397980.25731892199057
1.85-1.890.32461170.25672136225364
1.89-1.950.26991250.2612345247071
1.95-20.29031180.25952594271278
2-2.070.28451420.25322808295085
2.07-2.140.27291590.24783062322193
2.14-2.230.31571570.23363199335697
2.23-2.330.25651350.23943267340298
2.33-2.450.29121750.22523277345298
2.45-2.60.26861840.22143198338298
2.6-2.80.24971680.21993280344899
2.8-3.090.24771540.21393298345298
3.09-3.530.23311620.18853291345399
3.53-4.440.21531960.16793302349899
4.44-19.480.23571650.19323290345596
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)
10.54810.2748-0.11170.36160.19330.66230.0169-0.0541-0.15680.044-0.0072-0.0080.0735-0.0244-0.04830.03880.0054-0.03120.1131-0.06570.1275-5.408-0.588617.0973
21.0058-0.0897-0.04740.17680.20270.425-0.04960.12370.28980.01680.1197-0.0417-0.0430.12870.77340.06740.0151-0.06430.1178-0.01010.2091-5.21913.93315.0999
30.3224-0.3341-0.07090.39810.3691.70540.05230.01190.0907-0.03360.0914-0.2147-0.1540.37180.21110.13420.0386-0.00010.25140.0440.306712.75184.57510.0734
40.3330.5712-0.15730.9803-0.270.07440.04210.36140.0004-0.4010.0145-0.04070.21480.13020.05750.31520.15460.06020.46760.10240.207410.4828-7.6362-3.2565
50.0913-0.15040.0880.2471-0.14450.08430.0314-0.0827-0.13970.0555-0.042-0.13870.05330.1089-0.30260.07150.0615-0.0410.22050.02960.12615.3228-5.06516.527
61.12690.0281-0.43620.462-0.24911.4646-0.05160.133-0.0612-0.0844-0.07540.00720.13450.0902-1.15680.06140.0319-0.03680.0961-0.02770.0955-0.0342-2.10583.4946
70.1686-0.0505-0.10820.08070.0830.10820.0150.0425-0.055-0.0503-0.04880.05350.04170.01830.00530.17530.09330.04420.11230.02170.09634.209-7.88174.2797
80.69050.13130.27960.5411-0.01520.6764-0.09140.08330.20140.06260.03950.0034-0.1744-0.02180.08880.0930.02240.00280.04630.05970.08733.319640.540517.8618
90.2420.0334-0.08570.3492-0.15590.90140.02730.0936-0.1233-0.056-0.0721-0.20960.33070.1553-0.0590.17390.01550.02130.11650.02870.103836.882835.09956.6711
100.5649-0.2905-0.88680.18950.50071.44340.00630.1649-0.0711-0.0104-0.11330.06090.1057-0.0639-0.47660.23450.0116-0.09750.17890.0890.26322.954732.6363-5.2603
110.8292-0.1806-0.12150.46150.41671.14160.03960.24540.0442-0.14170.01610.0546-0.3682-0.15190.16480.1490.0229-0.00250.12170.04440.082928.903444.54092.7624
120.9241-0.3246-0.07940.26920.16020.3039-0.0219-0.07880.2225-0.0347-0.06660.0985-0.0385-0.1-0.22660.05490.0271-0.01810.1229-0.10740.1572-4.28912.551215.116
130.0458-0.0226-0.02730.07350.04020.02790.0107-0.01640.04090.0227-0.0680.1269-0.0082-0.0686-0.06260.1098-0.04620.08280.2342-0.17350.3194-12.75039.742825.6592
140.00550.0012-0.00180.0026-0.00190.0016-0.0350.052-0.032-0.0278-0.05-0.03370.00440.0118-0.00020.69420.04920.11710.5908-0.06560.63846.2756-0.408632.9845
151.1188-0.8219-1.13820.67630.82261.1609-0.0839-0.4085-0.12660.3442-0.0436-0.03660.22260.031-0.2870.2804-0.1056-0.04620.288-0.02170.16864.84639.472239.9513
160.0763-0.1215-0.03650.31240.12770.0581-0.0231-0.04440.00750.13430.02990.02960.02610.0664-0.11350.1465-0.06190.05910.2044-0.09370.12981.68920.650537.893
172.39810.1134-0.03020.27790.37621.20780.10230.14440.2275-0.0225-0.19870.2081-0.1457-0.2509-0.72430.06970.00370.03480.1724-0.09560.1621-4.28821.759620.4308
183.2776-0.0823-0.52081.61271.53711.525-0.0262-0.3946-0.26490.3478-0.13650.16030.3219-0.07190.25090.1585-0.07860.08840.1845-0.05850.1555-4.48358.25633.9242
190.0941-0.09890.03330.65430.03970.0220.0098-0.0562-0.04780.2376-0.10720.20750.0862-0.1736-0.74860.1701-0.08160.09450.2141-0.13810.1966-5.880519.411133.1185
201.82061.03120.70591.24450.58620.80460.05960.0973-0.1847-0.01620.0139-0.18520.2460.1080.33460.26030.04320.07110.07270.00930.098734.206526.361216.1997
210.6172-0.6570.51330.7999-0.52310.4489-0.1284-0.03630.04660.051-0.0708-0.30630.02890.1425-0.39820.12370.04490.05080.06910.04910.169135.130930.977329.0724
220.20330.260.02340.58670.46691.5669-0.06330.05620.078-0.2847-0.08480.10890.0761-0.2988-0.83610.24340.0126-0.01920.09180.01250.160120.973325.287630.0905
230.2587-0.1005-0.0550.11460.07790.19610.0125-0.00710.01180.0120.03840.0020.0152-0.02720.66420.04650.0148-0.03280.03970.0120.069927.140331.47932.9021
240.15190.1403-0.05270.394-0.10590.1539-0.04220.07550.0052-0.2219-0.0092-0.11110.1489-0.0045-0.27080.233-0.02770.02530.05260.00210.108727.562920.947132.9723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )A3 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 47 )A27 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 85 )A48 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 97 )A86 - 97
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 107 )A98 - 107
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 141 )A108 - 141
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 157 )A142 - 157
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 26 )B3 - 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 157 )B78 - 157
12X-RAY DIFFRACTION12chain 'C' and (resid 3 through 22 )C3 - 22
13X-RAY DIFFRACTION13chain 'C' and (resid 23 through 45 )C23 - 45
14X-RAY DIFFRACTION14chain 'C' and (resid 46 through 54 )C46 - 54
15X-RAY DIFFRACTION15chain 'C' and (resid 55 through 77 )C55 - 77
16X-RAY DIFFRACTION16chain 'C' and (resid 78 through 97 )C78 - 97
17X-RAY DIFFRACTION17chain 'C' and (resid 98 through 117 )C98 - 117
18X-RAY DIFFRACTION18chain 'C' and (resid 118 through 131 )C118 - 131
19X-RAY DIFFRACTION19chain 'C' and (resid 132 through 157 )C132 - 157
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 26 )D1 - 26
21X-RAY DIFFRACTION21chain 'D' and (resid 27 through 45 )D27 - 45
22X-RAY DIFFRACTION22chain 'D' and (resid 46 through 117 )D46 - 117
23X-RAY DIFFRACTION23chain 'D' and (resid 118 through 130 )D118 - 130
24X-RAY DIFFRACTION24chain 'D' and (resid 131 through 157 )D131 - 157

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