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- PDB-9e69: Antibody 5E10 -

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Basic information

Entry
Database: PDB / ID: 9.0E+69
TitleAntibody 5E10
Components
  • (Light Chain of antibody 5E10) x 2
  • Heavy Chain of antibody 5E10
  • Heavy chain of antibody 5E10
KeywordsIMMUNE SYSTEM / antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsZhou, T. / Sao-Fong Cheung, C. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Structure / Year: 2025
Title: The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody.
Authors: Reda Rawi / Nicholas C Morano / Crystal Sao-Fong Cheung / Haijuan Du / Jason Gorman / Madhu Prabhakaran / Jordan E Becker / Tatsiana Bylund / Sam Charaf / Xuejun Chen / Myungjin Lee / Darcy ...Authors: Reda Rawi / Nicholas C Morano / Crystal Sao-Fong Cheung / Haijuan Du / Jason Gorman / Madhu Prabhakaran / Jordan E Becker / Tatsiana Bylund / Sam Charaf / Xuejun Chen / Myungjin Lee / Darcy R Harris / Adam S Olia / Li Ou / Lingshu Wang / Shuishu Wang / Baoshan Zhang / Masaru Kanekiyo / Adrian B McDermott / Tongqing Zhou / Lawrence Shapiro / Peter D Kwong /
Abstract: The N terminus of the H3 subtype of influenza virus hemagglutinin is ∼10 residues longer than the N termini of most other hemagglutinins. As conserved, exposed, and linear regions may be good ...The N terminus of the H3 subtype of influenza virus hemagglutinin is ∼10 residues longer than the N termini of most other hemagglutinins. As conserved, exposed, and linear regions may be good vaccine targets, we investigated the vaccine utility of the extended H3-N terminus. First, we identified antibody 5E10, for which structure and binding analyses revealed recognition of the H3-N terminus. Second, we immunized mice with immunogens incorporating the H3-N terminus, boosted with hemagglutinin trimer, and isolated antibodies from immunogen-elicited B cells that bound both H3-N terminus and hemagglutinin trimer. However, hemagglutinin-complex structures of two such antibodies, 3864-6 and 3864-10, that neutralized H3-influenza strains, revealed only peripheral recognition of the hemagglutinin N terminus. Collectively, these results reveal the N terminus of H3 hemagglutinin to be a suboptimal vaccine target and suggest that-in addition to being conserved, flexible, and accessible-other factors influence the elicitation of potent broadly neutralizing responses.
History
DepositionOct 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 4, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of antibody 5E10
L: Light Chain of antibody 5E10
A: Heavy Chain of antibody 5E10
B: Light Chain of antibody 5E10


Theoretical massNumber of molelcules
Total (without water)99,6614
Polymers99,6614
Non-polymers00
Water00
1
H: Heavy chain of antibody 5E10
L: Light Chain of antibody 5E10


Theoretical massNumber of molelcules
Total (without water)49,8432
Polymers49,8432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-31 kcal/mol
Surface area19800 Å2
MethodPISA
2
A: Heavy Chain of antibody 5E10
B: Light Chain of antibody 5E10


Theoretical massNumber of molelcules
Total (without water)49,8182
Polymers49,8182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-30 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.969, 93.969, 107.667
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Antibody Heavy chain of antibody 5E10


Mass: 25413.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light Chain of antibody 5E10


Mass: 24429.383 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 Heavy Chain of antibody 5E10


Mass: 25231.430 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: Antibody Light Chain of antibody 5E10


Mass: 24586.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: JCSG1 A8 (#8) 0.2 M sodium acetate 20% PEG3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 30869 / % possible obs: 97.68 % / Redundancy: 5.1 % / Biso Wilson estimate: 80 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.049 / Net I/σ(I): 31.6
Reflection shellResolution: 2.633→2.727 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 2965 / CC1/2: 0.6 / CC star: 0.866 / Rpim(I) all: 0.684 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→38.06 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 39.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1563 5.08 %
Rwork0.2182 --
obs0.2195 30791 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 0 0 0 6436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046607
X-RAY DIFFRACTIONf_angle_d0.8169038
X-RAY DIFFRACTIONf_dihedral_angle_d15.32902
X-RAY DIFFRACTIONf_chiral_restr0.0491063
X-RAY DIFFRACTIONf_plane_restr0.0071131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.720.35261420.342563X-RAY DIFFRACTION94
2.72-2.810.361380.31992686X-RAY DIFFRACTION99
2.81-2.930.36961450.29782690X-RAY DIFFRACTION99
2.93-3.060.33531350.29622623X-RAY DIFFRACTION97
3.06-3.220.33341420.32812709X-RAY DIFFRACTION99
3.22-3.420.33071550.28692663X-RAY DIFFRACTION99
3.42-3.690.27461420.25922688X-RAY DIFFRACTION99
3.69-4.060.27481500.24362700X-RAY DIFFRACTION99
4.06-4.640.2121300.20142604X-RAY DIFFRACTION96
4.65-5.840.2041460.18212659X-RAY DIFFRACTION98
5.85-38.060.19461380.16582643X-RAY DIFFRACTION97
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)
10.23870.008-0.23890.0606-0.10830.2926-0.54260.4632-0.12050.4578-0.11340.00270.4496-0.2159-0.00931.0429-0.19040.1770.5868-0.02640.8011.888741.4232-11.548
20.7089-0.2967-0.73390.26180.14580.9931-0.33970.0823-0.06060.5157-0.24220.05490.1577-0.0035-0.5420.9009-0.14240.01930.43380.17970.665613.34644.0363-6.0586
30.1680.0236-0.06770.24210.15750.1466-0.1059-0.20040.36910.1977-0.34530.45140.40660.4923-0.0171.1901-0.1198-0.23271.07240.38021.043429.861951.72262.3294
40.004-0.009-0.00830.27860.07840.0108-0.2008-0.153-0.13940.35440.18580.4739-0.27330.3193-0.00041.753-0.2285-0.22111.5390.1710.788730.836552.253211.6426
50.30270.1248-0.22540.3401-0.35780.35180.0513-0.1309-0.1340.0211-0.4993-0.0428-0.33120.295-0.00040.68510.1273-0.01920.79270.08090.69511.22377.521632.9435
60.1274-0.0717-0.06780.18870.13220.1039-0.313-0.04550.114-0.2531-0.1477-0.1208-0.32480.7149-0.32880.8009-0.09260.15031.41550.64921.06441.09579.620611.0446
70.0790.02850.05220.00080.00840.0204-0.1679-0.0309-0.3078-0.3156-0.51410.2136-0.2282-0.1715-0.0231.2750.1131-0.03840.48540.06790.80863.83539.44578.2363
80.0710.02590.07190.0302-0.12740.3841-0.3323-0.28460.16440.09470.03420.0356-0.5316-0.2865-0.00020.97560.1884-0.21510.5816-0.08510.7525-0.160213.875216.6755
90.0582-0.01690.0362-0.0018-0.01540.0232-0.1908-0.17380.1936-0.12560.1123-0.1541-0.37190.1742-00.84340.0356-0.17460.54860.02870.6985.815.611313.4819
101.56490.01490.590.73210.62230.7604-0.54310.0950.2818-0.9545-0.22190.21610.01020.5487-1.50170.97130.08950.25860.69480.53170.355525.21726.23126.23
110.0954-0.01540.04260.0003-0.01030.0368-0.04590.3928-0.21510.0007-0.0036-0.2429-0.30540.017-0.00061.24790.09670.04471.06130.26591.155525.58644.27961.2141
120.09050.07790.0680.06430.07310.0273-0.20410.25480.1271-0.4608-0.10980.13660.21910.4147-0.00341.34790.37430.15091.20920.20470.879632.4136-0.0539-3.2477
130.2415-0.01060.23330.3683-0.45320.52910.22520.22640.14010.052-0.5624-0.01270.47120.3382-0.00010.7571-0.1014-0.00970.85170.06790.709311.205946.7167-29.0477
140.0194-0.01470.00570.04530.07270.0754-0.2054-0.073-0.33050.16810.0555-0.06470.21260.6768-0.00870.88410.0524-0.06281.46040.59251.196240.962744.5096-7.3786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 61 )
2X-RAY DIFFRACTION2chain 'B' and (resid 62 through 128 )
3X-RAY DIFFRACTION3chain 'B' and (resid 129 through 187 )
4X-RAY DIFFRACTION4chain 'B' and (resid 188 through 208 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 109 )
6X-RAY DIFFRACTION6chain 'H' and (resid 110 through 214 )
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 18 )
8X-RAY DIFFRACTION8chain 'L' and (resid 19 through 75 )
9X-RAY DIFFRACTION9chain 'L' and (resid 76 through 91 )
10X-RAY DIFFRACTION10chain 'L' and (resid 92 through 139 )
11X-RAY DIFFRACTION11chain 'L' and (resid 140 through 171 )
12X-RAY DIFFRACTION12chain 'L' and (resid 172 through 207 )
13X-RAY DIFFRACTION13chain 'A' and (resid 1 through 109 )
14X-RAY DIFFRACTION14chain 'A' and (resid 110 through 213 )

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