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- PDB-7tri: Human antibody S8V1-172 in complex with the influenza hemagglutin... -

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Basic information

Entry
Database: PDB / ID: 7tri
TitleHuman antibody S8V1-172 in complex with the influenza hemagglutinin head domain of A/Sydney/05/1997(H3N2)
Components
  • Hemagglutinin
  • S8V1-172 Fab heavy chain
  • S8V1-172 Fab kappa light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / influenza / antibody / neutralizing / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsMcCarthy, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Plos Biol. / Year: 2023
Title: A new class of antibodies that overcomes a steric barrier to cross-group neutralization of influenza viruses.
Authors: Simmons, H.C. / Watanabe, A. / Oguin Iii, T.H. / Van Itallie, E.S. / Wiehe, K.J. / Sempowski, G.D. / Kuraoka, M. / Kelsoe, G. / McCarthy, K.R.
History
DepositionJan 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Hemagglutinin
Y: S8V1-172 Fab kappa light chain
Z: S8V1-172 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9116
Polymers81,1523
Non-polymers1,7603
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.700, 94.700, 248.840
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Hemagglutinin


Mass: 32836.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Sydney/5/1997(H3N2))
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Q8C9
#2: Antibody S8V1-172 Fab kappa light chain


Mass: 23231.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody S8V1-172 Fab heavy chain


Mass: 25083.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
Has ligand of interestN

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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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M tris(hydroxymethyl)aminomethane pH 8.5 and 25% (w/v) poly(ethylene glycol) 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.6→49.56 Å / Num. obs: 15613 / % possible obs: 99.46 % / Redundancy: 2 % / Biso Wilson estimate: 117.69 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.04592 / Net I/σ(I): 12.72
Reflection shellResolution: 3.6→3.729 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3232 / Num. unique obs: 1543 / CC1/2: 0.709 / CC star: 0.911 / % possible all: 99.87

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XPZ, 6MHR, 6E4X

6xpz

6mhr

6e4x


Resolution: 3.6→49.56 Å / SU ML: 0.4992 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4627
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2682 789 5.05 %
Rwork0.2329 14822 -
obs0.2347 15611 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 118.51 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5403 0 150 0 5553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295682
X-RAY DIFFRACTIONf_angle_d0.60517730
X-RAY DIFFRACTIONf_chiral_restr0.0713892
X-RAY DIFFRACTIONf_plane_restr0.0051977
X-RAY DIFFRACTIONf_dihedral_angle_d5.0764828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.820.33351140.29472429X-RAY DIFFRACTION99.84
3.82-4.120.33071500.26482421X-RAY DIFFRACTION99.73
4.12-4.530.26231400.23612417X-RAY DIFFRACTION99.69
4.53-5.190.24371180.21312449X-RAY DIFFRACTION99.53
5.19-6.530.26851310.24412495X-RAY DIFFRACTION99.66
6.54-49.560.24481360.21122611X-RAY DIFFRACTION98.71
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)
12.333139727933.80868457006-4.986530428676.54400231297-4.753233944497.255073931850.6030953392262.227158682780.959476581049-0.9952824987291.06488838320.0884050837183-0.12680199659-0.838772633332-1.966574416211.131406222830.1537597651960.1612281093931.672755165180.1167976470111.2283786377412.337-18.453-3.087
21.899068552891.73910588167-1.195354996334.74807319594-3.591913595752.78064462218-0.4693094184280.876205452190.476934229666-0.5096770326740.2334153590061.125646999431.25794808494-0.489548024061-0.1320255123861.27194034986-0.2178595226730.1247636814781.06902612289-0.1199603704851.04236483727.705-32.3777.2
30.92977527120.03602111851290.5549423361216.10818212383-3.492470971592.55170453895-0.2832779273710.321876331833-0.0981414275799-0.2614816249250.487854339775-0.3188596348550.5286533901790.295525928562-0.02853469057010.886946021353-0.05368936418460.03233757927761.112762093980.008891129187780.96806723988510.897-29.09718.102
41.39047202631.28233984595-1.265624849665.0738545512-2.478341909563.05567459413-0.2946425313150.17055133685-0.168412063884-0.6004167679630.1755552732170.4361376279270.788704684106-0.1611360638080.05080187406031.095778680060.005273396688340.03999694146711.08794684554-0.1323107597761.153032260197.373-44.66418.333
51.805179554990.263405361181-0.1396923870484.900058811270.216513363671.98627998145-0.3551268987650.467455034021-0.4597649538-1.226384533180.369775250175-0.5356123568340.796815473791-0.2145253685280.3150750302431.186110262260.09596495546570.08162018748831.2054062341-0.1076600364740.99500032252916.25-48.87510.991
63.64313875065-0.174691114408-1.298750575246.478911437072.280900778496.03523592877-0.1871859242650.128071674975-0.359560348362-0.2739554156870.6071570929-0.3497037131140.6725226382250.4200050582550.2722946245131.141767072720.1012172714680.08392606708881.090834347840.06239294368051.1284226797318.199-47.83427.475
72.60821160864-0.00892568112893-0.1296818880165.351005985830.5577333917843.7447849521-0.564310011890.01814413261170.383160031518-0.4588203502080.438442614861-0.816228276712-0.2124789442670.6448729324240.1939329645520.909865251380.1157606962520.1371068074811.233579823990.2566313267991.0348705894416.392-40.71922.018
84.33722058587-0.36059620053-1.746294938528.95578691056-4.920205907885.5449709255-0.6962855051330.14412145835-1.07664108833-0.9978193092720.00277036551207-0.9037036757930.678900300576-0.09815293358660.6024551966140.717022493093-0.04580844685260.1043287476131.01778450677-0.1262563197470.8895332189613.886-36.9238.333
96.509091133440.002903495548441.314356486777.19846834538-4.850649112765.43939978851-0.5305784314592.077522162-0.0412056735574-1.44118987931-0.727718199386-0.08382625076480.619500437793-0.8194259193730.2782189288861.17404308249-0.01568982633090.1443871072841.612881269590.1453247610151.0882606546713.489-17.132-6.424
102.107652292664.86955151016-3.903700587987.21805584408-3.00971594422.64104069829-0.6207396129441.74829764206-0.254140148285-2.017498181060.417618188059-1.27200159363-0.478996000721-0.4907758641540.6273975944131.308687092520.0899442584980.2460215895161.711751159740.2117961900041.2568303816823.984-16.089-6.518
115.65950853472-5.61351662889-1.490534594835.691863726731.43635951610.416335700897-0.51848770361.254126123782.0503117170.2017425776260.133417990031-0.3659877410710.178720945155-1.404606080060.4340680291481.65291877617-0.3729316163630.01662115078941.52415436225-0.06878964602571.5089399170630.446-8.434-0.423
129.127230444251.538312603210.06289327285777.53626323802-1.487691173088.247335507960.03271241020040.7338416968160.522512587337-0.6250678759890.1176857408250.1856451554360.6386470710290.0359035264182-0.1939381559350.818317940322-0.06255282288940.002330714582620.7643781501290.09438962553810.686939366897-17.596-48.05132.312
133.292759320622.57297524709-1.553007236326.88113317538-3.212479767773.62694297414-0.4344368484760.0773973182634-0.0755559954549-0.7904967965270.371451639848-0.3515195175240.3893871893990.07631970736730.1232806876560.5979766613230.0283044460749-0.09652898234710.6390567382360.04381482904730.755290562406-26.495-59.51844.129
141.61132178465-0.181502910030.6510505417533.35235362651-1.34489697867.39028526861-0.03171555055630.1470238613990.225089232676-0.3699513222960.1953407532880.929470675573-0.0099151881944-0.671206848781-0.2594067334280.748879582409-0.047660732332-0.2212355420880.8593389347230.02080684592560.96575030949-42.497-68.09753.377
151.287190602810.505866090122-0.3226810566334.33407691862-1.329539454966.804667660440.192622295424-0.233516463066-0.297927944804-0.218434137744-0.27380217396-0.3910439237380.3374350124510.587324513788-0.01062026649930.5739975286590.0651906022852-0.05322708861370.9686647205190.04838741006990.887839040327-4.67-49.77351.313
162.12168548758-1.52652750968-1.613380849944.29650922858-1.722257516313.72960709141-0.01596732775980.6501037103-0.2536234971890.04126864695740.01280293111461.095458473350.5681884192220.2175620918150.1575610950230.6572355800870.269288457656-0.03532710041051.268295339230.06625995901510.723118613048-30.076-71.81160.595
171.878256174971.24524179161-0.8779598807348.422731931535.081887466174.78367681273-0.0522798301038-0.100058421925-0.4059372536990.05421375966030.0104907727217-0.3884288571720.335144285480.3883826298480.007778130890270.8525050824370.0686661006057-0.05566298044960.8482353315010.1086980641730.750844807284-25.758-73.6657.027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 41:65 )B41 - 65
2X-RAY DIFFRACTION2( CHAIN B AND RESID 66:89 )B66 - 89
3X-RAY DIFFRACTION3( CHAIN B AND RESID 90:104 )B90 - 104
4X-RAY DIFFRACTION4( CHAIN B AND RESID 105:165 )B105 - 165
5X-RAY DIFFRACTION5( CHAIN B AND RESID 166:184 )B166 - 184
6X-RAY DIFFRACTION6( CHAIN B AND RESID 185:214 )B185 - 214
7X-RAY DIFFRACTION7( CHAIN B AND RESID 215:245 )B215 - 245
8X-RAY DIFFRACTION8( CHAIN B AND RESID 246:275 )B246 - 275
9X-RAY DIFFRACTION9( CHAIN B AND RESID 276:288 )B276 - 288
10X-RAY DIFFRACTION10( CHAIN B AND RESID 289:308 )B289 - 308
11X-RAY DIFFRACTION11( CHAIN B AND RESID 327:330 )B327 - 330
12X-RAY DIFFRACTION12( CHAIN Y AND RESID 1:75 )Y1 - 75
13X-RAY DIFFRACTION13( CHAIN Y AND RESID 76:127 )Y76 - 127
14X-RAY DIFFRACTION14( CHAIN Y AND RESID 128:211 )Y128 - 211
15X-RAY DIFFRACTION15( CHAIN Z AND RESID 1:119 )Z1 - 119
16X-RAY DIFFRACTION16( CHAIN Z AND RESID 120:144 )Z120 - 144
17X-RAY DIFFRACTION17( CHAIN Z AND RESID 145:224 )Z145 - 224

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