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- PDB-4r8w: Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in comp... -

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Basic information

Entry
Database: PDB / ID: 4r8w
TitleCrystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a neutralizing antibody CT149
Components
  • (Hemagglutinin) x 2
  • Heavy chain of neutralizing antibody CT149
  • Light chain of neutralizing antibody CT149
KeywordsIMMUNE SYSTEM / Influenza A Virus / Hemagglutinin / neutralizing antibody
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 Å
AuthorsWu, Y. / Shi, Y. / Qi, J. / Gao, G.F.
CitationJournal: Nat Commun / Year: 2015
Title: A potent broad-spectrum protective human monoclonal antibody crosslinking two haemagglutinin monomers of influenza A virus
Authors: Wu, Y. / Cho, M. / Shore, D. / Song, M. / Choi, J. / Jiang, T. / Deng, Y.Q. / Bourgeois, M. / Almli, L. / Yang, H. / Chen, L.M. / Shi, Y. / Qi, J. / Li, A. / Yi, K.S. / Chang, M. / Bae, J.S. ...Authors: Wu, Y. / Cho, M. / Shore, D. / Song, M. / Choi, J. / Jiang, T. / Deng, Y.Q. / Bourgeois, M. / Almli, L. / Yang, H. / Chen, L.M. / Shi, Y. / Qi, J. / Li, A. / Yi, K.S. / Chang, M. / Bae, J.S. / Lee, H. / Shin, J. / Stevens, J. / Hong, S. / Qin, C.F. / Gao, G.F. / Chang, S.J. / Donis, R.O.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of neutralizing antibody CT149
L: Light chain of neutralizing antibody CT149
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2907
Polymers103,6274
Non-polymers6643
Water45025
1
A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of neutralizing antibody CT149
L: Light chain of neutralizing antibody CT149
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of neutralizing antibody CT149
L: Light chain of neutralizing antibody CT149
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of neutralizing antibody CT149
L: Light chain of neutralizing antibody CT149
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,87121
Polymers310,88012
Non-polymers1,9919
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)126.856, 126.856, 409.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-601-

HOH

21B-602-

HOH

31B-603-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin /


Mass: 34993.559 Da / Num. of mol.: 1 / Fragment: UNP residues 19-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Anhui/1-BALF_RG45/2013(H7N9))
Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024E3P0
#2: Protein Hemagglutinin /


Mass: 20442.463 Da / Num. of mol.: 1 / Fragment: UNP residues 340-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Anhui/1-BALF_RG45/2013(H7N9))
Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024E3P0, UniProt: A0A024E2M1*PLUS

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Antibody , 2 types, 2 molecules HL

#3: Antibody Heavy chain of neutralizing antibody CT149


Mass: 24429.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody Light chain of neutralizing antibody CT149


Mass: 23761.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Sugars / Non-polymers , 2 types, 28 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 30% v/v PEG 4000, 60mM Divalents, pH 8.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.795→50 Å / Num. all: 31761 / Num. obs: 31761 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 66.4 Å2
Reflection shellResolution: 2.795→2.9 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4KOL and 4DN3

4kol

4dn3


Resolution: 2.795→48.405 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.311 1606 5.06 %RANDOM
Rwork0.2624 ---
all0.265 31755 --
obs0.265 31755 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.795→48.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5608 0 42 25 5675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045773
X-RAY DIFFRACTIONf_angle_d0.787804
X-RAY DIFFRACTIONf_dihedral_angle_d15.4422101
X-RAY DIFFRACTIONf_chiral_restr0.034851
X-RAY DIFFRACTIONf_plane_restr0.0031025
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7949-2.88510.36951380.3007269898
2.8851-2.98820.36151340.30362709100
2.9882-3.10780.34381500.29152726100
3.1078-3.24930.29871400.29022737100
3.2493-3.42050.3261570.27752707100
3.4205-3.63480.31931490.27112735100
3.6348-3.91530.33921520.25682733100
3.9153-4.30910.28311520.23662752100
4.3091-4.93210.26251340.2413273399
4.9321-6.21180.34081560.2592278599
6.2118-48.41270.29711440.2628283497
Refinement TLS params.Method: refined / Origin x: 55.7892 Å / Origin y: -16.1559 Å / Origin z: -21.1885 Å
111213212223313233
T0.3915 Å2-0.0004 Å2-0.0578 Å2-0.3307 Å2-0.006 Å2--0.4178 Å2
L0.3599 °2-0.0933 °2-0.0603 °2-0.2062 °20.1215 °2--0.1572 °2
S-0.1043 Å °0.0805 Å °0.0479 Å °-0.0484 Å °-0.0807 Å °0.0506 Å °-0.0562 Å °0.0251 Å °-0.0259 Å °
Refinement TLS groupSelection details: all

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