[English] 日本語
Yorodumi
- PDB-6zqq: Structure of the Pmt3-MIR domain with bound ligands -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of endoplasmic reticulum unfolded protein response / fungal-type cell wall biogenesis / 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 ...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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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