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- PDB-7la8: O6 variable lymphocyte receptor ectodomain bound to 3-HSO3-Gal-4GlcNAc -

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Basic information

Entry
Database: PDB / ID: 7la8
TitleO6 variable lymphocyte receptor ectodomain bound to 3-HSO3-Gal-4GlcNAc
ComponentsO6 variable lymphocyte receptor
KeywordsIMMUNE SYSTEM/IMMUNOGEN / VLR / glycosylation / sulfated glycan / glycan antigen / IMMUNE SYSTEM / IMMUNE SYSTEM-IMMUNOGEN complex
Function / homologyBIOTIN
Function and homology information
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8965 Å
AuthorsBernard, S.M. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Commun Biol / Year: 2021
Title: Novel lamprey antibody recognizes terminal sulfated galactose epitopes on mammalian glycoproteins.
Authors: McKitrick, T.R. / Bernard, S.M. / Noll, A.J. / Collins, B.C. / Goth, C.K. / McQuillan, A.M. / Heimburg-Molinaro, J. / Herrin, B.R. / Wilson, I.A. / Cooper, M.D. / Cummings, R.D.
History
DepositionJan 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: O6 variable lymphocyte receptor
B: O6 variable lymphocyte receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,15410
Polymers37,3542
Non-polymers1,8008
Water3,585199
1
A: O6 variable lymphocyte receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7697
Polymers18,6771
Non-polymers1,0926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: O6 variable lymphocyte receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3853
Polymers18,6771
Non-polymers7082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.255, 107.255, 63.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEU(chain 'A' and (resid 1 through 139 or resid 141 through 172))AA1 - 1392 - 140
12PROPRO(chain 'A' and (resid 1 through 139 or resid 141 through 172))AA141 - 172142 - 173
21LEULEU(chain 'B' and (resid 1 through 139 or resid 141 through 172))BB1 - 1392 - 140
22PROPRO(chain 'B' and (resid 1 through 139 or resid 141 through 172))BB141 - 172142 - 173

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Components

#1: Protein O6 variable lymphocyte receptor


Mass: 18676.947 Da / Num. of mol.: 2 / Mutation: K18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Polysaccharide 3-O-sulfo-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 463.412 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalp[3S]b1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5_3*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp3SO3]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 2.4 M (NH4)2SO4, 0.1 M Bicine pH 9.0, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.896→38.2 Å / Num. obs: 28496 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.2779525002 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.048 / Rsym value: 0.114 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4560 / CC1/2: 0.559 / Rpim(I) all: 0.855 / Rsym value: 1.67

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RVX

1rvx


Resolution: 1.8965→37.92 Å / SU ML: 0.260465048734 / Cross valid method: FREE R-VALUE / σ(F): 1.33614351418 / Phase error: 24.0854108122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229055608869 1421 4.98859048622 %
Rwork0.184332239793 27064 -
obs0.186476030987 28485 99.8177804254 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.2747945708 Å2
Refinement stepCycle: LAST / Resolution: 1.8965→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 112 199 2901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01506359446782774
X-RAY DIFFRACTIONf_angle_d1.393073900523823
X-RAY DIFFRACTIONf_chiral_restr0.0724518358619456
X-RAY DIFFRACTIONf_plane_restr0.00896904232167475
X-RAY DIFFRACTIONf_dihedral_angle_d14.03261451181639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8965-1.96430.3545623795481330.3099111349752695X-RAY DIFFRACTION99.6125396266
1.9643-2.04290.2881333055651670.2875670838932634X-RAY DIFFRACTION99.6797153025
2.0429-2.13590.2922060049651430.2302279532442700X-RAY DIFFRACTION99.6844319776
2.1359-2.24850.2659513277271460.2069497877122696X-RAY DIFFRACTION100
2.2485-2.38940.2226148189031480.1916919699572692X-RAY DIFFRACTION99.9296270232
2.3894-2.57380.2308467322721270.1736240156952716X-RAY DIFFRACTION99.8595012294
2.5738-2.83270.2068049428191510.1629678704152710X-RAY DIFFRACTION99.965059399
2.8327-3.24250.2056237311281370.165381289632695X-RAY DIFFRACTION99.8589562764
3.2425-4.08440.2069688822911290.143584472982742X-RAY DIFFRACTION99.9651810585
4.0844-37.920.2235550188821400.1961873678562784X-RAY DIFFRACTION99.6931469485
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)
11.702933030442.06385812507-2.461736017296.14975138895-1.122609898014.564579536950.0574880866234-0.0560215718750.05083324303610.158764432896-0.290364577507-0.570626356872-0.1223010236430.318375520590.2280143363220.26672141948-0.000308720494832-0.01757682098860.3912054735940.01827116464020.330601026149-6.1166457662620.45287865625.9543925318
22.731407944710.04400664389170.1478817258477.22419317453-2.567063562174.96015595549-0.1174842443910.153012409230.1350609375780.345401684903-0.0553383215618-0.193056898204-0.07891072646840.06275074974860.3679517949840.212853842119-0.04005534745130.0009571432584060.2963126864740.0004511669854550.291106555639-11.690601823218.308321665327.5013040783
37.688144635561.8985358841-3.58479195275.30436484321-4.621657010077.909025492990.218684607014-0.3479800127760.2982516506480.131565544232-0.13618985303-0.1190698046150.1992740195810.232356405660.01437827015730.256373722403-0.0680365743234-0.04042806672190.279393889948-0.01008565918960.253960693656-16.10831554819.6964119355631.7857201425
46.42952600905-3.29330368496-0.02894454848829.56369316459-2.349013469448.74599309522-0.173798109854-0.2345193002180.7264538783130.53144860760.0271207559618-0.238490028099-0.6506011967490.215186102910.2207371601510.2174875313480.00947817761555-0.06451968576120.247171434497-0.03672643274230.353033861735-21.172766380523.370789201728.7147159999
56.765850524080.504605122947-0.8628853906534.71613106904-1.350490957563.83950916998-0.08903037582140.0673109797854-0.06351740012230.0724186168464-0.08129678934560.1072720539510.038137921558-0.03762160996910.1045655109780.267676778968-0.0319332753588-0.06047135411590.245838047758-0.04089983715050.215782899192-21.738373678212.340535108226.9405309893
62.53874283434-0.775801254547-0.007268416122875.32557643624-1.437427348974.16394451865-0.03628402524570.03842071068990.220668575705-0.03799161240080.1495802408250.105287734874-0.218770251358-0.13109977736-0.02349325826740.21246235265-0.0419312282798-0.01701213504760.29627107442-0.003016195538730.281419848638-22.262908304714.321470556621.7378840905
79.54452773058-6.846159985226.304175270225.02882132701-4.279176003424.708058709430.0577335151931-0.185175339068-0.3683297002970.655841672280.03951726555660.6804691496840.15135068104-0.493980465397-0.103700356570.3261808039910.009167607548980.00678758319240.303683855363-0.01651174296170.388157873476-31.632352634110.019955311226.4646920951
83.894628702130.377759018036-0.9309212716256.09948201735-1.919807099211.53698004621-0.02761111070140.03846688113420.02080405926990.289850893117-0.049847485541-0.122201000381-0.0677370989837-0.1180170112080.0369033618540.2727117871470.0156487994097-0.04195427021490.238841838366-0.03991070741220.150489223824-27.63227603047.9322747303920.6837663594
98.270444052261.96150006839-4.261727275555.087369394771.756889532254.7123002016-0.1840226104250.00603727770554-0.2001099219380.1853567337120.1128867153260.392649331645-0.00698793673326-0.2718495997660.0494081476070.3006578223420.0140306104529-0.0656462429690.317281769420.002833070417020.352314111348-36.20631291547.4153157667920.9521351019
105.381474460312.51369744536-0.4305964759626.670597508571.002887863314.00547148318-0.1833560430530.402463694366-0.189962068134-0.05173906203720.223182806683-0.2635968917550.18516916145-0.1368351891230.1108594676460.2865676908170.0134379219687-0.03488643644930.288734771189-0.01160882551040.23522998863-22.33057051187.1082481501910.683774563
118.3147061323-2.56904720825.066681473659.41318217679-7.432891996847.092277531120.3029444955070.884910185053-1.38230769915-0.5184980796040.1636335208660.5596812896210.2843901759360.228386542199-0.4935599125410.4434592115090.0437675026591-0.07072623166510.354157899718-0.06932949574370.431912201191-30.6545455031-5.0383467249819.2113142768
127.799232497972.34009397141-4.237617035547.63718441748-1.689471817295.66717128545-0.111450918447-0.205113094681-0.2166994619360.4576885341250.003332147748120.600391324090.324163830259-0.60691609712-0.2264563328890.341045617937-0.05257646645320.02186634794270.308522409846-0.0172240592250.396470951419-40.2019498037-0.6907766367625.414141585
131.976414938991.454555183990.2120470971638.19674546767-3.872090608753.97173844107-0.01118410032970.0507875329299-0.157406944662-0.445970632338-0.286909772046-0.4683102417670.2025677980810.4277143917790.1723864599790.3136833991440.01638145283540.0274502650020.359714966090.007765595417440.343617641618-13.7351155819-12.844206708745.6541728778
143.027275491193.5772233816-1.20578417446.26956835583-3.26812077573.281005806420.0259817854768-0.206010116528-0.3106270716040.061041736458-0.0112223390650.06324162086790.530464436343-0.08179134876770.2375432085540.2256936828840.06900785419110.02347054811520.242702634447-0.01413994779640.299141395381-20.7969965112-15.870510975248.961081684
156.43424478459-5.351717761434.024451516999.23892794547-5.839058168394.152981860340.4331454926390.4251503915110.0679178837267-0.627475136069-0.3740058590480.1262761959430.1670962316450.40998342863-0.01075859458770.3269294656490.03848459742570.05107029051240.294229303801-0.03630593625560.322289848682-18.5050311428-2.54086777341.9624251079
163.1077419247-0.556413259831-0.3134623135363.24059871227-1.129342536742.66912921574-0.02496959463830.00694868052749-0.0367584902355-0.04306394102650.004842231136410.06342364929860.0302914585187-0.0310365684587-0.07603658479910.28060029880.005938267522130.009241488440510.239900556-0.02809145051140.271793554759-26.0510631281-6.3255862084946.1106732388
174.404655061183.92696663699-2.007750101279.70062117841-2.386340444273.382512968230.0133194134186-0.196659707058-0.1494681211520.193173047401-0.09013778298660.05425294627740.1091237165980.1259933377750.04473082143950.2810855771460.03396548115260.01014265632970.281597868879-0.03986809100890.324151591164-26.0239313594-4.4811762338851.939497502
186.034208523965.16999991111-4.574353175884.99296978672-2.845144793959.11534786885-0.1058218097680.3463780974620.120419299063-0.8875689763020.11572152220.3165426826450.0655242752294-0.3544071951330.0178032933750.2673232830110.0230723007947-0.003016491886940.25519250923-0.03638656402160.411589063153-33.0611342383.0294917530847.3859383367
194.00847434342-0.274304530236-0.4506717830835.68187561477-2.526671871631.92436080198-0.083363919523-0.0778928004492-0.161745372515-0.100084151966-0.116489605866-0.04788205862150.00367380645736-0.02299278251260.1739877327820.287276154272-0.02022355065450.009649349330190.27966187724-0.05909068707190.193031951373-28.52624657473.4172164372553.1512156043
205.33211583661-0.6503985435413.541187554233.58479350969-3.26133556527.90437585946-0.07653727325780.02385503304420.3351089922510.0448257198422-0.04780463295420.489393225816-0.438992412076-0.2262228049140.03902649993320.236781394190.008556478211790.03126509187220.24439919597-0.03746706302410.30623272182-36.2033363317.2258348272552.8393423542
217.96573478035-5.439593389031.305128505366.923356451350.2309126378871.30254123946-0.0774166813647-0.500509107179-0.06808151556810.07470041050270.240796659531-0.151651362877-0.227354667304-0.106914316806-0.02405583131120.307823917384-0.0279882422780.02454899520030.324427005101-0.02831276966650.229806985959-23.76575006142.4296746918662.8279136647
229.469794073423.74141813377-7.802885088224.70360532257-5.875292843059.044856844830.16387493154-0.7959099178061.35896091580.4468794598280.102956109608-0.119101864229-0.4556657915760.574103610644-0.1538974667710.349908232382-0.0381565866808-0.04746786112210.390466141964-0.09114511947250.48157645844-26.311749050216.620298286354.6816914755
238.54580485272-4.170170463377.474858958853.94669968014-5.70038177929.40643790824-0.0774732292370.04280287693280.603454859166-0.427961729878-0.07259955977830.2557938256590.00359181788596-0.5283017113080.2480727530390.364233990394-0.00450892077227-0.01829207667630.223928509147-0.05632681109190.423730449247-36.607977869916.221771563448.6357212438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 45 )
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 55 )
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 74 )
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 88 )
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 98 )
8X-RAY DIFFRACTION8chain 'A' and (resid 99 through 117 )
9X-RAY DIFFRACTION9chain 'A' and (resid 118 through 129 )
10X-RAY DIFFRACTION10chain 'A' and (resid 130 through 148 )
11X-RAY DIFFRACTION11chain 'A' and (resid 149 through 157 )
12X-RAY DIFFRACTION12chain 'A' and (resid 158 through 172 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 24 )
14X-RAY DIFFRACTION14chain 'B' and (resid 25 through 35 )
15X-RAY DIFFRACTION15chain 'B' and (resid 36 through 45 )
16X-RAY DIFFRACTION16chain 'B' and (resid 46 through 74 )
17X-RAY DIFFRACTION17chain 'B' and (resid 75 through 88 )
18X-RAY DIFFRACTION18chain 'B' and (resid 89 through 98 )
19X-RAY DIFFRACTION19chain 'B' and (resid 99 through 117 )
20X-RAY DIFFRACTION20chain 'B' and (resid 118 through 129 )
21X-RAY DIFFRACTION21chain 'B' and (resid 130 through 148 )
22X-RAY DIFFRACTION22chain 'B' and (resid 149 through 157 )
23X-RAY DIFFRACTION23chain 'B' and (resid 158 through 172 )

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