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- PDB-6zqq: Structure of the Pmt3-MIR domain with bound ligands -

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Basic information

Entry
Database: PDB / ID: 6zqq
TitleStructure of the Pmt3-MIR domain with bound ligands
ComponentsPMT3 isoform 1
KeywordsPEPTIDE BINDING PROTEIN / carbohydrate-binding module / MIR domain / protein-O-mannosylation / beta-trefoil
Function / homology
Function and homology information


dolichyl-phosphate-mannose-protein mannosyltransferase Pmt5p-Pmt3p dimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt3p dimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / dolichyl-phosphate-mannose-protein mannosyltransferase Pmt1p-Pmt2p dimer complex / : / protein O-linked mannosylation / protein O-linked glycosylation / membrane => GO:0016020 / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Glycosyl transferase family 39/83 / Glycosyltransferase 39-like / Protein O-mannosyl-transferase, C-terminal four TM domain / Dolichyl-phosphate-mannose-protein mannosyltransferase / C-terminal four TMM region of protein-O-mannosyltransferase / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily
Similarity search - Domain/homology
Dolichyl-phosphate-mannose--protein mannosyltransferase / Dolichyl-phosphate-mannose--protein mannosyltransferase 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWild, K. / Chiapparino, A. / Hackmann, Y. / Mortensen, S. / Sinning, I.
Funding support1items
OrganizationGrant numberCountry
German Research Foundation (DFG)
CitationJournal: Elife / Year: 2020
Title: Functional implications of MIR domains in protein O -mannosylation.
Authors: Chiapparino, A. / Grbavac, A. / Jonker, H.R. / Hackmann, Y. / Mortensen, S. / Zatorska, E. / Schott, A. / Stier, G. / Saxena, K. / Wild, K. / Schwalbe, H. / Strahl, S. / Sinning, I.
History
DepositionJul 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PMT3 isoform 1
B: PMT3 isoform 1
C: PMT3 isoform 1
D: PMT3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6097
Polymers97,3334
Non-polymers2763
Water6,630368
1
A: PMT3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4252
Polymers24,3331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PMT3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4252
Polymers24,3331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PMT3 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4252
Polymers24,3331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PMT3 isoform 1


Theoretical massNumber of molelcules
Total (without water)24,3331
Polymers24,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.289, 64.306, 65.555
Angle α, β, γ (deg.)107.900, 99.850, 99.720
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PMT3 isoform 1


Mass: 24333.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PMT3, GI526_G0005657 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q4I2, UniProt: P47190*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6, 0.26 M calcium acetate and 15% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.9→52.933 Å / Num. obs: 61932 / % possible obs: 95.5 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 14.14
Reflection shellResolution: 1.9→1.99 Å / Num. unique obs: 5998 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MAL

3mal


Resolution: 1.9→52.933 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 3076 4.97 %
Rwork0.1742 58850 -
obs0.1763 61926 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.87 Å2 / Biso mean: 40.9634 Å2 / Biso min: 18.92 Å2
Refinement stepCycle: final / Resolution: 1.9→52.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6483 0 18 368 6869
Biso mean--49.07 43.79 -
Num. residues----806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92970.37391300.3229260993
1.9297-1.96140.30381530.2902253691
1.9614-1.99520.30951470.2524264895
1.9952-2.03150.23951450.2329262495
2.0315-2.07050.27211410.2287269695
2.0705-2.11280.30491440.2214270096
2.1128-2.15870.28411320.2181263195
2.1587-2.2090.24851400.2056270496
2.209-2.26420.25281620.1921264896
2.2642-2.32540.24021050.1903269495
2.3254-2.39390.2451480.183267696
2.3939-2.47110.24781430.1794261594
2.4711-2.55940.25171420.1773263494
2.5594-2.66190.2311510.1769272297
2.6619-2.78310.23241470.1885270297
2.7831-2.92980.22221220.1778273697
2.9298-3.11330.24311330.1722273597
3.1133-3.35370.17171310.1717268696
3.3537-3.69110.19031460.1591265395
3.6911-4.2250.16351370.1332277299
4.225-5.32220.1711250.1278272997
5.3222-52.9330.22481520.1773270097
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)
15.17450.8679-1.89192.8823-0.65912.1876-0.15190.4315-0.1961-0.54440.1621-0.02110.3774-0.356-0.01340.3208-0.0371-0.06350.2332-0.00730.1918-41.1406-32.789.0656
24.6407-0.6013-1.88453.4780.90493.85750.0172-0.05570.0487-0.0883-0.0268-0.5190.13580.2830.02060.18610.0394-0.02040.16310.02780.1938-28.5888-29.828613.9946
35.97645.7692-0.93449.3229-1.15972.29560.527-0.71880.20320.9799-0.34220.3113-0.1485-0.1677-0.25160.2889-0.01060.04180.36370.00690.3541-49.0514-26.768123.5666
44.01510.6206-0.79853.6798-1.04562.12860.00990.07490.4513-0.15520.13830.0582-0.0355-0.1241-0.10730.2064-0.0016-0.01830.1960.01250.262-38.6037-22.23612.2753
52.83370.13421.22155.7265-0.8915.1740.01090.62940.4617-0.6709-0.0565-0.2304-0.00160.06860.02210.3326-0.00090.05890.24980.04710.2365-31.2287-23.60752.942
63.44190.9387-4.53345.0861-0.55566.0338-0.5657-0.0931-0.52260.0664-0.08470.12240.9840.18610.29110.4676-0.096600.27380.0170.4132-48.6305-40.731414.1056
71.8751-0.2706-0.42833.8057-0.92653.4363-0.12730.05490.06650.02870.18960.34670.1638-0.54660.00490.19030.0109-0.02730.34260.05530.2208-23.0771-42.786930.2899
86.5281-1.4986-2.08677.3142-0.59078.71170.2850.55791.2145-0.1998-0.3161-0.3544-0.80430.093-0.04350.2578-0.006-0.00890.26730.08510.5241-9.2702-29.547126.8504
94.29890.6592-1.92743.6644-1.57878.70250.0164-0.44180.56650.5390.31160.3056-0.8227-0.5425-0.36090.32170.15150.04190.41370.00960.4061-26.3477-33.92536.0743
105.0542-0.0161-0.57923.2489-0.84723.6436-0.167-0.27430.21260.25240.16770.04050.0004-0.31320.02250.23190.0413-0.01060.27720.02910.1914-17.4389-42.544238.0649
116.55480.5499-3.35684.6584-1.73873.5797-0.0232-0.09250.09830.18090.019-0.039-0.0045-0.1590.02420.17460.0166-0.0480.20920.01690.2115-14.1017-45.328834.6994
122.97560.7631-1.80522.9567-0.94552.5137-0.21980.3049-0.1979-0.36030.0853-0.0653-0.0282-0.16640.12450.3433-0.0017-0.02670.2959-0.0470.1652-15.588-47.4879-14.6862
135.0266-1.8731-1.39356.27592.50125.9513-0.47110.18-1.2393-0.0147-0.24580.71090.9614-0.54390.55590.4707-0.04390.15560.2767-0.06240.4963-21.0035-61.0922-2.1847
147.74320.8939-1.33254.07530.44064.0526-0.40880.4229-0.9144-0.6240.0358-0.41090.46690.05460.32870.4810.02450.12730.2811-0.04930.3226-8.4655-55.8909-16.252
155.12541.0691-0.58213.4325-2.11053.1643-0.0975-0.3267-0.01470.08310.0907-0.16760.10970.1936-0.00460.27320.0328-0.0290.2345-0.020.1586-10.845-49.0404-1.302
166.9346-0.28031.11664.7716-0.36732.0131-0.05260.20410.2154-0.5579-0.015-0.52460.07030.61840.1440.365-0.01690.11060.2963-0.04210.2798-3.1442-43.2598-16.2564
177.8572.3559-4.03243.2554-1.6293.09680.02050.41250.2244-0.05570.21170.3461-0.1821-0.351-0.19670.30620.0271-0.0620.3275-0.03980.1985-21.1583-44.4673-4.5029
183.86480.827-4.04242.5268-1.64494.4565-0.06280.44990.0364-0.26730.15640.2116-0.0471-0.3326-0.11110.27850.0018-0.00930.2230.00540.3959-46.5212-58.360514.0202
196.2451-1.5972-2.16362.44261.66443.24260.0819-0.28240.23660.16650.12370.2167-0.0807-0.0994-0.1560.22320.00220.06110.15930.02870.3783-45.9907-58.815327.8093
205.3551-0.2731-0.65744.4991-2.70368.09110.0725-0.1193-0.0297-0.138-0.1389-0.5841-0.12730.64030.05230.28810.04450.05740.2895-0.0370.4597-29.5827-62.461412.8107
215.18481.5725-0.7575.8698-1.74984.32730.0541-0.2529-0.50460.3777-0.0132-0.0910.28910.11390.00040.30220.05880.0550.21870.05430.4242-41.3767-66.597627.9695
227.2222-1.84586.05122.9995-1.27569.82430.02870.2917-0.655-0.31090.1626-0.00990.35130.1668-0.22730.3538-0.01520.04740.21-0.05470.4471-41.2477-70.405414.747
236.6368-5.4474-2.72574.52372.84736.82480.27540.7227-0.3638-0.6982-0.24520.4509-0.2422-0.1007-0.05420.5010.0205-0.03510.3863-0.00470.497-44.9837-62.32141.3305
241.5782-0.0246-0.01181.5670.58093.2088-0.0959-0.0675-0.49340.10350.08050.30540.4163-0.31970.0670.3091-0.01510.0730.22810.05120.4888-50.9797-67.104824.0828
255.81210.8296-3.30382.3883-1.3874.88880.02210.2963-0.2501-0.02850.01080.44780.18-0.2873-0.11230.2530.0121-0.05230.1976-0.00730.396-47.7262-64.214613.6102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 331 through 356 )A331 - 356
2X-RAY DIFFRACTION2chain 'A' and (resid 357 through 385 )A357 - 385
3X-RAY DIFFRACTION3chain 'A' and (resid 386 through 410 )A386 - 410
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 488 )A411 - 488
5X-RAY DIFFRACTION5chain 'A' and (resid 489 through 520 )A489 - 520
6X-RAY DIFFRACTION6chain 'A' and (resid 521 through 532 )A521 - 532
7X-RAY DIFFRACTION7chain 'B' and (resid 331 through 385 )B331 - 385
8X-RAY DIFFRACTION8chain 'B' and (resid 386 through 410 )B386 - 410
9X-RAY DIFFRACTION9chain 'B' and (resid 411 through 447 )B411 - 447
10X-RAY DIFFRACTION10chain 'B' and (resid 448 through 502 )B448 - 502
11X-RAY DIFFRACTION11chain 'B' and (resid 503 through 532 )B503 - 532
12X-RAY DIFFRACTION12chain 'C' and (resid 331 through 385 )C331 - 385
13X-RAY DIFFRACTION13chain 'C' and (resid 386 through 410 )C386 - 410
14X-RAY DIFFRACTION14chain 'C' and (resid 411 through 447 )C411 - 447
15X-RAY DIFFRACTION15chain 'C' and (resid 448 through 488 )C448 - 488
16X-RAY DIFFRACTION16chain 'C' and (resid 489 through 513 )C489 - 513
17X-RAY DIFFRACTION17chain 'C' and (resid 514 through 532 )C514 - 532
18X-RAY DIFFRACTION18chain 'D' and (resid 331 through 356 )D331 - 356
19X-RAY DIFFRACTION19chain 'D' and (resid 357 through 385 )D357 - 385
20X-RAY DIFFRACTION20chain 'D' and (resid 386 through 410 )D386 - 410
21X-RAY DIFFRACTION21chain 'D' and (resid 411 through 447 )D411 - 447
22X-RAY DIFFRACTION22chain 'D' and (resid 448 through 459 )D448 - 459
23X-RAY DIFFRACTION23chain 'D' and (resid 460 through 472 )D460 - 472
24X-RAY DIFFRACTION24chain 'D' and (resid 473 through 502 )D473 - 502
25X-RAY DIFFRACTION25chain 'D' and (resid 503 through 530 )D503 - 530

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