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- PDB-7trh: Human antibody K03.28 in complex with the influenza hemagglutinin... -

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Basic information

Entry
Database: PDB / ID: 7trh
TitleHuman antibody K03.28 in complex with the influenza hemagglutinin head domain of A/California/07/2009(H1N1)(X-181)
Components
  • Hemagglutinin
  • K03.28 Fab heavy chain
  • K03.28 Fab lambda light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / influenza / antibody / neutralizing / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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 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
G: Hemagglutinin
H: K03.28 Fab heavy chain
B: K03.28 Fab lambda light chain


Theoretical massNumber of molelcules
Total (without water)73,9753
Polymers73,9753
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-27 kcal/mol
Surface area28410 Å2
Unit cell
Length a, b, c (Å)75.830, 43.650, 96.910
Angle α, β, γ (deg.)90.000, 105.033, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Hemagglutinin


Mass: 25198.215 Da / Num. of mol.: 1 / Fragment: head domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/reassortant/NYMC X-181(California/07/2009 x NYMC X-157)(H1N1)
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C9EL84
#2: Antibody K03.28 Fab heavy chain


Mass: 25628.646 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 K03.28 Fab lambda light chain


Mass: 23148.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% (w/v) poly(ethylene glycol) 1500

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→46.8 Å / Num. obs: 24401 / % possible obs: 98.33 % / Redundancy: 2 % / Biso Wilson estimate: 77.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03992 / Net I/σ(I): 14.93
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 0.3816 / Num. unique obs: 2401 / CC1/2: 0.771 / CC star: 0.933

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UBE, 6E56, 4HK0, 4WUK

3ube

6e56

4hk0

4wuk


Resolution: 3→46.8 Å / SU ML: 0.4575 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 623 5.01 %
Rwork0.2017 11816 -
obs0.2038 12439 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.52 Å2
Refinement stepCycle: LAST / Resolution: 3→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4971 0 0 0 4971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285103
X-RAY DIFFRACTIONf_angle_d0.62576952
X-RAY DIFFRACTIONf_chiral_restr0.045762
X-RAY DIFFRACTIONf_plane_restr0.0064891
X-RAY DIFFRACTIONf_dihedral_angle_d4.9176698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.32851530.28892910X-RAY DIFFRACTION98.17
3.3-3.780.32061550.24792932X-RAY DIFFRACTION98.66
3.78-4.760.22961550.18322950X-RAY DIFFRACTION98.57
4.76-46.80.19361600.17323024X-RAY DIFFRACTION98.03
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)
13.39276649769-3.104709217091.230329310083.356626371820.07228017246883.22198946124-0.104286878208-0.2651421347041.27391759945-0.7126472822830.113401706165-1.0798199797-0.9511095951460.0883992475696-0.167814848410.9548956870940.179862600569-0.1129994256491.07643176441-0.4895246377320.80648039675230.915199192510.182074721816.9517491893
21.504514992151.1201645975-0.4525445438122.83626250925-0.5666831133932.812188810830.378731616683-0.45506535404-0.218369255731-0.230747107753-0.107337347776-0.318530119261-0.855584065675-0.8285121247730.6175551192490.8146727010930.103764582564-0.1369948553361.0501009584-0.4012798488160.62886936279932.083117385511.237189265816.7089756605
35.893381886682.910183106274.940664578924.064776025720.06789913278868.04518135272-0.395879461392-0.5438306046650.2692704445390.1230099449-1.009153584150.0263253420677-1.01062538111-0.751838868374-3.813359543640.6914114718670.0224808656462-0.05086314055961.594139754580.003091177482710.46626282673520.78090363930.17446007545316.0797825735
42.624635060060.08538227808551.274274689841.35207234279-0.6463468955880.953008628542-0.0950558617757-0.408319484398-0.262137693622-0.1164994094950.00663006195309-0.150900172695-0.300972511449-0.320068404893-0.0002511745628020.5692397641770.09451542257260.04896383118510.689616549638-0.02433443084930.62602033418131.482648916-3.458098061045.90384609029
51.257813241610.758014902655-0.1110605401251.129501766751.006640194771.701520356570.206827926248-0.862126167735-0.3424281714050.244584378809-0.140096808757-0.01796026207060.0768205827471-0.3279939429390.0001783781997530.6668299645270.007529139251710.02353456641760.8003969047550.1580887035140.76693682609126.4122731571-9.5985289572510.9313074881
63.337272458370.6786537074531.352625818960.9536537569160.8648216951322.29236946078-0.00574578311974-0.274065532651-0.642531521920.07540792075420.1070773399470.1397970470240.32450382775-0.2460839382960.0003277954541560.496873503081-0.01200208719220.06481628754860.3706745593870.08380435372390.570674082772-1.87047012351-7.31485211894-17.7821964877
70.9111707448230.1125913082130.04776729145180.2207381338930.1465865232140.723841075245-0.00926737141947-0.218464987943-0.280976164051-0.2774619665890.327993960022-0.03037127181270.174702957891-0.001854166315840.0001325931387830.598377101786-0.1090101925260.002823753276520.484128314688-0.02305434563650.498467488027-2.389675318841.82516637784-24.3164190196
80.7511152747710.6925232087410.1769015357851.34199106036-0.4794937455570.606252584843-0.321846325458-0.112556327318-0.44133988496-0.56715878690.347082262685-0.463122289470.5758928692010.7654199108990.005708310340010.792142516636-0.169565074660.1284502388890.8892747866-0.01298545068660.6154449605-7.9822895692212.0352640045-46.0891775379
90.3342762735050.2753605351360.1445933433980.4975055558510.4541735004910.501765767008-0.3704640006880.709913757181-0.155207050369-0.9635107627650.09779752423970.05934159065240.3302610868890.0426916302919-0.0003002454911191.18416553448-0.2822271160010.07556024938830.983780808227-0.08080263412130.725395848375-9.9010938990913.4455390477-54.457900152
102.340153176710.8118605198121.143962778461.58407363715-0.4234780679731.68256293535-0.265461423844-0.2112043399750.740555173706-0.03634530269930.239251990059-0.2706762691640.07926105714390.160937772491-0.003668239853610.5090043370310.0678934637859-0.02978224741350.473588392877-0.172224490890.66475787204314.81654868369.9269204704-16.4990702781
111.76123828086-0.6608660225521.157124022670.739723291039-0.9204973015931.2567621895-0.202158946519-0.01561284876790.6892489652430.3663561337780.1344777722940.0057915014551-0.3238312955790.08937466981380.01855829318940.5903090772810.01402843191620.0007376168062260.496794074631-0.0606400785990.64898126291311.291125356512.0809026937-20.5225144119
121.723045350591.12125688623-0.2858750682523.24022252619-0.105643255861.84238369906-0.107021420991-0.1247020813430.0932934500606-0.160944276759-0.03822110702130.0981214145299-0.0111005749504-0.04266638413940.0003689245490430.633413549975-0.152793804147-0.03289288184730.6055104623810.05986764457130.51717647632-8.6747439383726.3245183241-40.4584784668
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'G' and (resid 57 through 71 )GA57 - 711 - 15
22chain 'G' and (resid 72 through 91 )GA72 - 9116 - 35
33chain 'G' and (resid 92 through 104 )GA92 - 10436 - 48
44chain 'G' and (resid 105 through 174 )GA105 - 17449 - 122
55chain 'G' and (resid 175 through 264 )GA175 - 264123 - 212
66chain 'H' and (resid 2 through 83 )HB2 - 831 - 82
77chain 'H' and (resid 84 through 147 )HB84 - 14783 - 141
88chain 'H' and (resid 148 through 188 )HB148 - 188142 - 182
99chain 'H' and (resid 189 through 228 )HB189 - 228183 - 222
1010chain 'B' and (resid 1 through 68 )BC1 - 681 - 68
1111chain 'B' and (resid 69 through 117 )BC69 - 11769 - 117
1212chain 'B' and (resid 118 through 214 )BC118 - 214118 - 214

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