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- PDB-5cjq: Crystal structure of a trimeric influenza hemagglutinin stem in c... -

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Basic information

Entry
Database: PDB / ID: 5cjq
TitleCrystal structure of a trimeric influenza hemagglutinin stem in complex with an broadly neutralizing antibody CR9114
Components
  • CR9114 heavy chain
  • CR9114 light chain
  • Designed influenza hemagglutinin stem #4900, HA1
  • Designed influenza hemagglutinin stem #4900, HA2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / trimer / influenza / immunogen / monoclonal / antibody / neutralizing / influenza vaccine / glycoprotein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyHemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Science / Year: 2015
Title: A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen.
Authors: Impagliazzo, A. / Milder, F. / Kuipers, H. / Wagner, M.V. / Zhu, X. / Hoffman, R.M. / van Meersbergen, R. / Huizingh, J. / Wanningen, P. / Verspuij, J. / de Man, M. / Ding, Z. / Apetri, A. / ...Authors: Impagliazzo, A. / Milder, F. / Kuipers, H. / Wagner, M.V. / Zhu, X. / Hoffman, R.M. / van Meersbergen, R. / Huizingh, J. / Wanningen, P. / Verspuij, J. / de Man, M. / Ding, Z. / Apetri, A. / Kukrer, B. / Sneekes-Vriese, E. / Tomkiewicz, D. / Laursen, N.S. / Lee, P.S. / Zakrzewska, A. / Dekking, L. / Tolboom, J. / Tettero, L. / van Meerten, S. / Yu, W. / Koudstaal, W. / Goudsmit, J. / Ward, A.B. / Meijberg, W. / Wilson, I.A. / Radosevic, K.
History
DepositionJul 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: CR9114 light chain
H: CR9114 heavy chain
A: Designed influenza hemagglutinin stem #4900, HA1
B: Designed influenza hemagglutinin stem #4900, HA2


Theoretical massNumber of molelcules
Total (without water)76,1934
Polymers76,1934
Non-polymers00
Water00
1
L: CR9114 light chain
H: CR9114 heavy chain
A: Designed influenza hemagglutinin stem #4900, HA1
B: Designed influenza hemagglutinin stem #4900, HA2

L: CR9114 light chain
H: CR9114 heavy chain
A: Designed influenza hemagglutinin stem #4900, HA1
B: Designed influenza hemagglutinin stem #4900, HA2

L: CR9114 light chain
H: CR9114 heavy chain
A: Designed influenza hemagglutinin stem #4900, HA1
B: Designed influenza hemagglutinin stem #4900, HA2


Theoretical massNumber of molelcules
Total (without water)228,57812
Polymers228,57812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)157.696, 157.696, 202.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Antibody CR9114 light chain


Mass: 22712.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody CR9114 heavy chain


Mass: 24423.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
#3: Protein Designed influenza hemagglutinin stem #4900, HA1


Mass: 7013.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Trichoplusia ni (cabbage looper)
#4: Protein Designed influenza hemagglutinin stem #4900, HA2


Mass: 22043.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Trichoplusia ni (cabbage looper)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M sodium citrate, pH 5.5, 1.64 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 11619 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rsym value: 0.1 / Net I/σ(I): 22
Reflection shellResolution: 3.6→50 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.96 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→38.85 Å / SU ML: 0.83 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 43.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.369 547 4.73 %
Rwork0.346 --
obs0.347 11557 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 0 0 4812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144918
X-RAY DIFFRACTIONf_angle_d2.4586664
X-RAY DIFFRACTIONf_dihedral_angle_d17.4331760
X-RAY DIFFRACTIONf_chiral_restr0.096744
X-RAY DIFFRACTIONf_plane_restr0.011859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.93830.47921320.41572703X-RAY DIFFRACTION99
3.9383-4.50750.42711410.38342747X-RAY DIFFRACTION100
4.5075-5.67610.38761380.36422757X-RAY DIFFRACTION100
5.6761-38.85640.30941360.30812803X-RAY DIFFRACTION98

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