[English] 日本語
Yorodumi
- PDB-6xkg: Crystal structure of 3-O-Sulfotransferase isoform 3 in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xkg
TitleCrystal structure of 3-O-Sulfotransferase isoform 3 in complex with 8mer oligosaccharide with 6S sulfation
ComponentsHeparan sulfate glucosamine 3-O-sulfotransferase 3A1
KeywordsTRANSFERASE / sulfotransferase / enzyme / PAPS / Heparan sulfate
Function / homology
Function and homology information


[heparan sulfate]-glucosamine 3-sulfotransferase 3 / [heparan sulfate]-glucosamine 3-sulfotransferase activity / : / glycosaminoglycan biosynthetic process / HS-GAG biosynthesis / sulfotransferase activity / branching involved in ureteric bud morphogenesis / Golgi membrane / membrane
Similarity search - Function
Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / P-NITROPHENOL / Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPedersen, L.C. / Liu, J. / Wander, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES102645 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL094463 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL144970 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128484 United States
CitationJournal: Rsc Chem Biol / Year: 2021
Title: Deciphering the substrate recognition mechanisms of the heparan sulfate 3- O -sulfotransferase-3.
Authors: Wander, R. / Kaminski, A.M. / Xu, Y. / Pagadala, V. / Krahn, J.M. / Pham, T.Q. / Liu, J. / Pedersen, L.C.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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
B: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
A: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,84517
Polymers62,4322
Non-polymers5,41315
Water12,376687
1
B: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,24510
Polymers31,2161
Non-polymers3,0299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6007
Polymers31,2161
Non-polymers2,3846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.760, 65.012, 92.235
Angle α, β, γ (deg.)90.000, 124.735, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-778-

HOH

21B-857-

HOH

DetailsThe biological assembly is unknown. Biophysical analysis is inconclusive but seems to indicate a monomer. In three different crystal forms, the same dimer is observed in the asymmetric unit.

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Heparan sulfate glucosamine 3-O-sulfotransferase 3A1 / Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 / h3-OST-3A


Mass: 31215.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HS3ST3A1, 3OST3A1, HS3ST3A, UNQ2551/PRO6180 / Plasmid: pGEX4T3 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -RIL
References: UniProt: Q9Y663, [heparan sulfate]-glucosamine 3-sulfotransferase 3

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1670.363 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-3-2-3-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 2129.743 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/4,8,7/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NCC/3=O_6*OSO/3=O/3=O]/1-2-3-2-3-2-1-4/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNAc6SO3]{}}}}}}}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 700 molecules

#4: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#5: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 15.5mg/ml 3ost3a, 4mM PAP, 5mM 8mer Nac/NS2S6S, 25mM Tris pH 7.5, 125mM NaCl, Reservoir: 0.1M Bicine and 10% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 5, 2019 / Details: varimaxHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 91530 / % possible obs: 97 % / Redundancy: 2.5 % / Biso Wilson estimate: 18.29 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.027 / Rrim(I) all: 0.053 / Net I/σ(I): 18.2
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 4216 / CC1/2: 0.748 / Rpim(I) all: 0.396 / Rrim(I) all: 0.583 / % possible all: 90.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8U

1t8u


Resolution: 1.55→32.86 Å / SU ML: 0.148 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 2000 2.19 %random selection
Rwork0.1638 89491 --
obs0.1642 91491 96.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 1.55→32.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 334 687 5205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01044764
X-RAY DIFFRACTIONf_angle_d1.06996491
X-RAY DIFFRACTIONf_chiral_restr0.0558732
X-RAY DIFFRACTIONf_plane_restr0.0073791
X-RAY DIFFRACTIONf_dihedral_angle_d14.941780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.24761230.22675541X-RAY DIFFRACTION84.35
1.59-1.630.2141370.20886070X-RAY DIFFRACTION92.17
1.63-1.680.22231380.21116210X-RAY DIFFRACTION94.11
1.68-1.730.25871400.19646298X-RAY DIFFRACTION95.63
1.73-1.790.20211430.18966385X-RAY DIFFRACTION96.77
1.79-1.860.22791450.18376457X-RAY DIFFRACTION97.82
1.86-1.950.18631450.17566489X-RAY DIFFRACTION98.24
1.95-2.050.21141450.17786480X-RAY DIFFRACTION98.25
2.05-2.180.20241450.15926514X-RAY DIFFRACTION98.45
2.18-2.350.19561460.16416518X-RAY DIFFRACTION98.41
2.35-2.590.20411460.16766563X-RAY DIFFRACTION98.88
2.59-2.960.17581480.16616605X-RAY DIFFRACTION98.99
2.96-3.730.16851480.14886589X-RAY DIFFRACTION99.18
3.73-32.860.14451510.14436772X-RAY DIFFRACTION99.7
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)
10.248058759957-0.119178493171-0.09092351581270.1460274291280.1049309093640.128914384203-0.0233502770824-0.0909818724859-0.05836506307670.04960893252210.0230849891193-0.02959991884270.0561270163566-0.0475761619512.88248815052E-80.151293806764-0.00203993172064-0.0003503189134410.135235751282-0.007326737211320.1306896672523.095747346-51.728712852363.4882041745
20.0911301955687-0.103747179897-0.05344172861520.1050572002530.01325612825530.0645445749443-0.1437085778350.0665904922653-0.3146428637640.07956529979950.03455871301370.04016026792470.257073255318-0.163535157568-0.00363275841540.192681350829-0.03318051733260.03208374709950.174920304672-0.01505826019940.165526940079.56194506659-57.738555915861.2524452544
30.6504427916140.0879979958486-0.03815426821090.4223281839610.01782569228020.327819250514-0.006015604349380.0495413255081-0.06214667113770.0101640792762-0.0005160797686750.001803345153660.0220502557651-0.168856262750.001885470012540.133420995156-0.003417095551830.01022550797730.144959646035-0.01992394967890.12078984807515.2118399133-51.130148656753.0442139785
40.6071865812390.0335143391076-0.5223458033160.579961526895-0.1802293141250.5009569608490.1136313181480.563573732312-0.361508094456-0.4869037034430.1600260755310.1124402931880.504100424054-0.2191796126140.2579369406980.289941697846-0.0352519561519-0.0627205774430.331886300806-0.1462799183790.29769396379712.3693729824-62.027977593929.8520786686
50.2438597409650.114663360339-0.1301650917910.1775327660710.01368075266770.0955206839061-0.09141868997890.168377434381-0.0598063375373-0.09436488286580.0416766729240.168030076219-0.0224513017373-0.1812669045520.0008283295716910.1635294426740.0210070208718-0.001819602321270.211372760821-0.002045063495380.1569521332097.8339686165-45.397099481344.8522629707
60.7938670574110.0473465942206-0.02775586207580.06444428983460.1198223124780.421530338481-0.004385110533340.119970048135-0.00125961820082-0.02752759280370.00526729655519-0.0374485208377-0.027740681090.0776684794914-0.000651803094540.147148381897-0.0005911998058290.01290466911810.133664993587-0.01406181857930.13983633553729.9759300188-48.171968337650.8847310285
70.332142937880.01334128706930.02897286219550.1424468049220.006220516967030.0551186640102-0.0001668344342520.4597654698380.113317533959-0.2663843100920.0266834081523-0.080074476248-0.297087311482-0.00349969530691-0.03212393911280.20854096879-0.009293487539550.01861424024050.283128054754-0.00162863687230.13095752515417.1348913232-43.322601786532.5660971775
80.2972132252630.106807982597-0.1840860244440.332202617218-0.1023032697710.081616654213-0.0439043870794-0.0309756043652-0.00619393473666-0.02378907922380.038112024394-0.09985323820340.00920599592470.01559215439016.40224552229E-80.141843115890.0179600828824-0.00229049632860.139270302405-0.00680715933580.17761281983753.0068484838-55.834142036968.7047380628
90.02991333513330.0111232890106-0.06494368188770.429663478158-0.07328318092670.106541240194-0.0867509588047-0.1872690737740.1117547216270.1037919032440.0914546137456-0.331651617196-0.05678653588860.237249624965-0.01682647979590.1584025127480.0101256379188-0.01505175738910.23659595573-0.0397028501680.25736843210761.401941017-49.751494704675.3114738316
100.163440490224-0.01461716235240.07336812737070.1467303203690.03379083116170.06356971210690.164590343001-0.450467431875-0.09972542157020.579731107314-0.114985906623-0.3970217434860.120441503948-0.05257629162720.03731005987940.388908911520.0076937837382-0.1289103349060.3049632033410.005069491232890.24197209571255.6451042835-51.840027129797.0924608276
110.0565075848747-0.0356005032447-0.02285698898970.2088314283430.02339596093750.0952099491263-0.192960490387-0.107482433159-0.01034815810.2420906484850.0739650358934-0.306081136314-0.1916572030550.18417397326-0.02100517418220.156409331985-0.0205657942997-0.06531705169180.233569321426-0.05698777728930.36332884519566.4750338137-43.712646881878.5170359537
120.644961120297-0.2312758512370.1855588628730.4453714091370.1804546729580.200109708389-0.0477360154443-0.1269292426940.1125978052060.087504747530.01762635857180.0221045891639-0.0874646318133-0.06723376342380.000538651543130.1528972059460.0106168997475-0.009029322603540.156039092324-0.0331953784840.15417160899841.6159164357-45.009748804977.1738654017
130.1211527065020.01038252782430.09787985809530.05029462890230.0044512479720.0775250939104-0.176770801019-0.2268580150070.2504364408810.304335825204-0.0212732654182-0.222301699164-0.278785032693-0.0658978631366-0.08862646591180.3235802172970.0535985387276-0.1256100908990.239557270806-0.09467576606010.28756359352156.9824519814-36.400187270692.1187883846
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 141 through 180 )BA141 - 1801 - 40
22chain 'B' and (resid 181 through 202 )BA181 - 20241 - 62
33chain 'B' and (resid 203 through 259 )BA203 - 25963 - 119
44chain 'B' and (resid 260 through 283 )BA260 - 283120 - 143
55chain 'B' and (resid 284 through 303 )BA284 - 303144 - 163
66chain 'B' and (resid 304 through 376 )BA304 - 376164 - 236
77chain 'B' and (resid 377 through 406 )BA377 - 406237 - 266
88chain 'A' and (resid 147 through 215 )AB147 - 2151 - 69
99chain 'A' and (resid 216 through 244 )AB216 - 24470 - 98
1010chain 'A' and (resid 245 through 290 )AB245 - 29099 - 141
1111chain 'A' and (resid 291 through 303 )AB291 - 303142 - 154
1212chain 'A' and (resid 304 through 376 )AB304 - 376155 - 227
1313chain 'A' and (resid 377 through 406 )AB377 - 406228 - 257

+
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