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- PDB-9b8g: 2C9 Fab antibody fragment against the E protein of the Yellow Fev... -

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Basic information

Entry
Database: PDB / ID: 9b8g
Title2C9 Fab antibody fragment against the E protein of the Yellow Fever virus
Components
  • 2C9 Fab heavy chain
  • 2C9 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Flavivirus / Yellow Fever
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsBalk, J. / Ting, Y.T. / Bibby, S. / Watterson, D. / Coulibaly, F.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1164216 Australia
National Health and Medical Research Council (NHMRC, Australia)APP2004582 Australia
CitationJournal: Nat Commun / Year: 2025
Title: A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity.
Authors: Summa Bibby / James Jung / Yu Shang Low / Alberto A Amarilla / Natalee D Newton / Connor A P Scott / Jessica Balk / Yi Tian Ting / Morgan E Freney / Benjamin Liang / Timothy Grant / Fasséli ...Authors: Summa Bibby / James Jung / Yu Shang Low / Alberto A Amarilla / Natalee D Newton / Connor A P Scott / Jessica Balk / Yi Tian Ting / Morgan E Freney / Benjamin Liang / Timothy Grant / Fasséli Coulibaly / Paul Young / Roy A Hall / Jody Hobson-Peters / Naphak Modhiran / Daniel Watterson /
Abstract: Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. ...Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. Here we use a chimeric virus platform to resolve the first high resolution cryo-EM structures of YFV. Stark differences in particle morphology and homogeneity are observed between vaccine and virulent strains of YFV, and these are found to have significant implications on antibody recognition and neutralisation. We identify a single residue (R380) in the YFV envelope protein that stabilises the virion surface, and leads to reduced exposure of the cross-reactive fusion loop epitope. The differences in virion morphology between YFV strains also contribute to the reduced sensitivity of the virulent YFV virions to vaccine-induced antibodies. These findings have significant implications for YFV biology, vaccinology and structure-based flavivirus antigen design.
History
DepositionMar 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: 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

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Assembly

Deposited unit
A: 2C9 Fab heavy chain
B: 2C9 Fab light chain
C: 2C9 Fab heavy chain
D: 2C9 Fab light chain
H: 2C9 Fab heavy chain
L: 2C9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,85113
Polymers146,2406
Non-polymers6127
Water4,450247
1
A: 2C9 Fab heavy chain
B: 2C9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7823
Polymers48,7472
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2C9 Fab heavy chain
D: 2C9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9394
Polymers48,7472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: 2C9 Fab heavy chain
L: 2C9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1316
Polymers48,7472
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.667, 125.329, 96.928
Angle α, β, γ (deg.)90.000, 93.947, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 42 or (resid 43...
d_2ens_1(chain "C" and (resid 1 through 42 or (resid 43...
d_3ens_1(chain "H" and (resid 1 through 98 or resid 100 through 222))
d_1ens_2(chain "B" and (resid 1 through 44 or (resid 45...
d_2ens_2(chain "D" and (resid 1 through 44 or (resid 45...
d_3ens_2(chain "L" and (resid 1 through 79 or (resid 80...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUGLYGLYAA1 - 985 - 102
d_12ens_1TYRTYRSERSERAA100 - 135104 - 139
d_13ens_1GLYGLYLYSLYSAA141 - 222145 - 226
d_21ens_1GLUGLUGLYGLYCC1 - 985 - 102
d_22ens_1TYRTYRSERSERCC100 - 135104 - 139
d_23ens_1GLYGLYLYSLYSCC141 - 222145 - 226
d_31ens_1GLUGLUGLYGLYHE1 - 985 - 102
d_32ens_1TYRTYRLYSLYSHE100 - 222104 - 226
d_11ens_2GLUGLUGLYGLYBB1 - 2125 - 216
d_21ens_2GLUGLUGLYGLYDD1 - 2125 - 216
d_31ens_2GLUGLUGLYGLYLF1 - 2125 - 216

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.399572635648, -0.916700203782, -0.00156372245083), (0.909895236173, -0.396812804415, 0.120955601121), (-0.111500529287, 0.0469077247276, 0.992656686538)50.1447345991, 33.9543664595, -65.8641846723
2given(-0.500584518039, 0.850622885619, -0.160797533441), (-0.852711557165, -0.516540332693, -0.0779043322161), (-0.149325619292, 0.0981162125334, 0.983908058846)-3.1287923589, 66.8316317173, -32.9748502328
3given(-0.391307287741, -0.91988819593, -0.0261593874026), (0.912050172305, -0.391448172591, 0.12219988287), (-0.122650274191, 0.02395903094, 0.992160710307)52.6486308155, 33.7171117837, -64.7331449765
4given(-0.485272839338, 0.853215971184, -0.191135496227), (-0.865709811486, -0.499527864314, -0.0319129295324), (-0.122706127389, 0.149981396481, 0.981044742614)-0.974944251842, 62.6462276763, -35.9193585539

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Components

#1: Antibody 2C9 Fab heavy chain


Mass: 24559.570 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Fabs digested using GST-HRV3C protease (GVHS/E) and cleaned up using protein A and GST resin.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNBF / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 2C9 Fab light chain


Mass: 24186.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Fabs digested using GST-HRV3C protease (GVHS/E) and cleaned up using protein A and GST resin.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNBF / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.3 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Aug 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.66→49.32 Å / Num. obs: 46392 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 40.38 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.321 / Rpim(I) all: 0.129 / Χ2: 0.99 / Net I/av σ(I): 8.3 / Net I/σ(I): 7.1
Reflection shellResolution: 2.66→2.75 Å / Redundancy: 7.3 % / Rmerge(I) obs: 3.141 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4537 / CC1/2: 0.403 / Rpim(I) all: 1.163 / Χ2: 1.02 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
AimlessCCP4 7.1.015data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→49.32 Å / SU ML: 0.3643 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.6512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 2291 4.94 %
Rwork0.2008 44043 -
obs0.2035 46334 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.11 Å2
Refinement stepCycle: LAST / Resolution: 2.66→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9917 0 31 247 10195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006310178
X-RAY DIFFRACTIONf_angle_d0.822113814
X-RAY DIFFRACTIONf_chiral_restr0.05091530
X-RAY DIFFRACTIONf_plane_restr0.00641758
X-RAY DIFFRACTIONf_dihedral_angle_d16.24283671
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.27809737607
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.34110125324
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.22764307469
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.948295694402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.720.32381490.29012748X-RAY DIFFRACTION99.52
2.72-2.780.33581410.27832738X-RAY DIFFRACTION99.72
2.78-2.850.3511310.27352748X-RAY DIFFRACTION99.83
2.85-2.930.33811610.2672738X-RAY DIFFRACTION99.93
2.93-3.010.33591390.26072701X-RAY DIFFRACTION99.89
3.01-3.110.30411520.25382740X-RAY DIFFRACTION99.97
3.11-3.220.30531550.24362762X-RAY DIFFRACTION99.93
3.22-3.350.31131600.22522717X-RAY DIFFRACTION100
3.35-3.50.27121230.20612767X-RAY DIFFRACTION100
3.5-3.690.26881180.20452764X-RAY DIFFRACTION99.97
3.69-3.920.27161510.19232748X-RAY DIFFRACTION100
3.92-4.220.20821260.16282783X-RAY DIFFRACTION100
4.22-4.650.18791440.13782740X-RAY DIFFRACTION100
4.65-5.320.1771370.14532775X-RAY DIFFRACTION100
5.32-6.70.21991600.1852754X-RAY DIFFRACTION100
6.7-49.320.25531440.19522820X-RAY DIFFRACTION99.9

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