[English] 日本語
Yorodumi
- PDB-3v0l: Crystal structure of the Fucosylgalactoside alpha N-acetylgalacto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v0l
TitleCrystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-Gal derived inhibitor (2GW)
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / GTA / ABO / CISAB MUTANT / ROSSMANN FOLD / "Semi-closed" CONFORMATION / GLYCOSYLTRANSFERASE / GLYCOPROTEIN / BLOOD GROUP ANTIGEN / UDP-GalNAc / METAL-BINDING / MANGANESE / Glycosylation / TRANSMEMBRANE / GOLGI APPARATUS / SECRETED / SIGNAL-ANCHOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-2GW / : / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsPalcic, M.M. / Jorgensen, R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Base-modified Donor Analogues Reveal Novel Dynamic Features of a Glycosyltransferase.
Authors: Jrgensen, R. / Pesnot, T. / Lee, H.J. / Palcic, M.M. / Wagner, G.K.
History
DepositionDec 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 8, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4474
Polymers34,6541
Non-polymers7933
Water3,693205
1
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8958
Polymers69,3082
Non-polymers1,5876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5180 Å2
ΔGint-57 kcal/mol
Surface area22380 Å2
MethodPISA
2
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8958
Polymers69,3082
Non-polymers1,5876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2190 Å2
ΔGint-48 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.430, 148.580, 78.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Histo-blood group ABO system transferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N- ...Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Histo-blood group A transferase / A transferase / Histo-blood group B transferase / B transferase / NAGAT / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form


Mass: 34654.008 Da / Num. of mol.: 1 / Fragment: Extracellular catalytic domain / Mutation: L266G, G268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AB0, ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-2GW / 5-phenyl-uridine-5'-alpha-d-galactosyl-diphosphate


Mass: 642.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N2O17P2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM MOPS pH 7, 50-200 mM AMMONIUM SULFATE, 50 mM MnCl2, AND 6-9% PEG-3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90772 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2009
Details: Multilayer mirror, curved to focus in the vertical (R = 400 m)
RadiationMonochromator: Bent silicon crystal, horizontally focusing (R = 12 m). Will be planar diamond monochromator.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90772 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 31515 / Num. obs: 31474 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.75-1.857.40.653.27349624740473799.9
1.85-27.40.385.544061455055505100
2-2.257.40.2029.94596362316231100
2.25-2.57.40.13514.09294303979397799.9
2.5-37.40.09119.583368245674567100
3-3.57.30.05629.271721323512351100
3.5-47.20.04735.62962913331333100
4-57.20.04138.8295181325132499.9
5-67.10.04436.784260600600100
6-106.80.04137.68461867767699.9
10-205.10.03938.45106520717383.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.7 Å
Translation2.5 Å19.7 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.3phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RIT

2rit


Resolution: 1.75→19.7 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.907 / SU ML: 0.29 / Isotropic thermal model: Isotropic+tls / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 15.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 945 3 %Random
Rwork0.1471 ---
obs0.1481 31450 99.97 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.713 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 100.62 Å2 / Biso mean: 21.896 Å2 / Biso min: 5.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.0291 Å2-0 Å20 Å2
2--0.0185 Å20 Å2
3---0.0105 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 48 205 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212428
X-RAY DIFFRACTIONf_angle_d1.8843317
X-RAY DIFFRACTIONf_chiral_restr0.151364
X-RAY DIFFRACTIONf_plane_restr0.011416
X-RAY DIFFRACTIONf_dihedral_angle_d13.784897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.75-1.84220.26991320.2043425643884388
1.8422-1.95760.17121340.1574433644704470
1.9576-2.10850.17261330.1331430744404440
2.1085-2.32040.1611350.1314434144764476
2.3204-2.65550.19811340.1379433344674467
2.6555-3.3430.18591360.1521438445204520
3.343-19.70120.15911410.1455454846894689
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)
13.6066-0.73171.14322.3077-1.10372.26210.12530.0783-0.12160.2019-0.2053-0.1096-0.09710.4690.05010.1084-0.0493-0.01690.17820.0250.129110.527-13.860533.7708
22.28680.0809-4.46760.0044-0.14688.8026-0.1697-0.206-0.13710.11180.08310.2364-0.3195-0.05510.01890.27010.01520.09510.2141-0.02310.20593.6923-2.258523.1827
32.32740.30760.08981.25220.1121.18640.0044-0.10910.1202-0.0257-0.0028-0.0892-0.1395-0.03670.00970.09430.00220.0060.0904-0.01130.11681.5928-10.470215.033
42.5588-1.7714-0.23295.5436-0.63081.0837-0.2201-0.32180.18020.26410.2472-0.2078-0.06880.0195-0.03490.092-0.0067-0.00070.14770.0010.112213.3699-19.74724.4954
51.77440.4056-1.61271.9817-0.76364.84660.11270.04550.01420.15530.06830.02350.1234-0.2504-0.18590.07260.0204-0.01890.07220.00690.087916.0943-28.392110.0116
61.78390.1572-0.26121.48690.27472.8520.02320.0469-0.0481-0.01680.0075-0.19680.15690.2352-0.03620.07690.02060.01150.0844-0.00240.114624.2406-21.04382.1037
71.481-0.4363-0.22651.33451.31485.52880.1716-0.02990.01030.01580.0679-0.15360.4154-0.0239-0.17080.086-0.0028-0.01980.0695-0.01240.091120.4936-29.81886.7717
82.3042-0.5488-1.34093.10292.8943.00970.0268-0.29480.03980.2460.2396-0.2160.18430.33520.0130.08990.06040.0210.1227-0.01930.090130.4185-28.5515-0.7929
90.91230.33910.24450.69360.60372.31540.02950.169-0.2004-0.18130.01380.04060.32290.1097-0.13050.1410.0124-0.02160.1257-0.03940.079723.2929-32.0783.1551
101.0416-0.87450.60653.8884-3.02265.02810.0080.3586-0.2489-0.41540.0509-0.04660.3919-0.3285-0.06030.2533-0.0198-0.00180.2894-0.06270.387810.2979-33.3816-1.8686
110.8681-0.1666-0.04560.52760.06521.98710.01620.03410.1397-0.07620.0141-0.047-0.12320.1287-0.02310.08040.02290.00920.06840.00240.095816.4008-20.72576.1395
121.0559-0.02050.34850.57960.16450.4210.02310.08150.1107-0.0182-0.05210.066-0.08430.03570.0190.0988-0.00420.01660.0879-0.00210.09496.1498-14.42177.8667
132.74011.30081.35213.0990.96893.8426-0.02820.0738-0.0582-0.3339-0.04150.1789-0.4466-0.42370.01540.1520.0402-0.0250.17240.03740.1485-4.9632-13.4856-7.1414
140.61240.53560.52291.09780.97362.82350.08180.10310.0091-0.2202-0.10890.3044-0.2271-0.5434-0.03960.1360.0352-0.0440.20480.00210.1401-8.9167-17.2883-4.9122
151.1595-0.49010.03721.1845-0.33090.80340.04240.0784-0.02780.034-0.0275-0.0684-0.03340.0443-0.01920.07560.00130.00430.07540.0140.0845.4038-19.8134.5416
165.27120.04540.71026.68060.5024.16230.2483-0.4017-0.82220.5905-0.04580.24740.6956-0.3952-0.04660.1612-0.0294-0.02840.15770.0340.16582.6057-32.21847.8506
173.0686-0.04933.25162.03040.60037.98510.16340.2185-0.1482-0.2950.0284-0.01870.3825-0.1137-0.28610.1568-0.0113-0.0020.1185-0.02640.13130.0177-30.9906-6.4532
180.89760.01530.50991.28970.34853.27430.00290.14930.0286-0.19330.0195-0.0258-0.0465-0.0398-0.01590.0810.00310.00470.11840.00750.0963-0.681-21.3062-1.8138
190.51490.57350.22392.5139-1.02070.95680.0183-0.08830.10320.0262-0.00540.0328-0.18350.0622-0.0150.13560.00190.01430.08850.01190.111913.297-6.42684.8795
201.99910.30340.03040.31610.45812.9630.0848-0.070.2438-0.1748-0.0782-0.1132-0.32440.2801-0.19650.1374-0.01590.05850.10920.01860.119216.9962-9.06516.8156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 65:76 )A65 - 76
2X-RAY DIFFRACTION2( CHAIN A AND RESID 77:82 )A77 - 82
3X-RAY DIFFRACTION3( CHAIN A AND RESID 83:98 )A83 - 98
4X-RAY DIFFRACTION4( CHAIN A AND RESID 99:111 )A99 - 111
5X-RAY DIFFRACTION5( CHAIN A AND RESID 112:122 )A112 - 122
6X-RAY DIFFRACTION6( CHAIN A AND RESID 123:143 )A123 - 143
7X-RAY DIFFRACTION7( CHAIN A AND RESID 144:154 )A144 - 154
8X-RAY DIFFRACTION8( CHAIN A AND RESID 155:163 )A155 - 163
9X-RAY DIFFRACTION9( CHAIN A AND RESID 164:177 )A164 - 177
10X-RAY DIFFRACTION10( CHAIN A AND RESID 181:203 )A181 - 203
11X-RAY DIFFRACTION11( CHAIN A AND RESID 204:218 )A204 - 218
12X-RAY DIFFRACTION12( CHAIN A AND RESID 219:241 )A219 - 241
13X-RAY DIFFRACTION13( CHAIN A AND RESID 242:250 )A242 - 250
14X-RAY DIFFRACTION14( CHAIN A AND RESID 251:262 )A251 - 262
15X-RAY DIFFRACTION15( CHAIN A AND RESID 263:274 )A263 - 274
16X-RAY DIFFRACTION16( CHAIN A AND RESID 275:279 )A275 - 279
17X-RAY DIFFRACTION17( CHAIN A AND RESID 280:293 )A280 - 293
18X-RAY DIFFRACTION18( CHAIN A AND RESID 294:318 )A294 - 318
19X-RAY DIFFRACTION19( CHAIN A AND RESID 319:335 )A319 - 335
20X-RAY DIFFRACTION20( CHAIN A AND RESID 336:345 )A336 - 345

+
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