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- PDB-6vmz: Crystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117 -

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Basic information

Entry
Database: PDB / ID: 6vmz
TitleCrystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / Influenza / H5 / CBS1117
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / apical plasma membrane / host cell surface receptor binding / 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 / 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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-R3P / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsAntanasijevic, A. / Durst, M.A. / Lavie, A. / Caffrey, M.
CitationJournal: Life Sci Alliance / Year: 2020
Title: Structure of avian influenza hemagglutinin in complex with a small molecule entry inhibitor.
Authors: Antanasijevic, A. / Durst, M.A. / Cheng, H. / Gaisina, I.N. / Perez, J.T. / Manicassamy, B. / Rong, L. / Lavie, A. / Caffrey, M.
History
DepositionJan 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
C: Hemagglutinin
E: Hemagglutinin
B: Hemagglutinin
D: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,20317
Polymers176,4876
Non-polymers2,71511
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30390 Å2
ΔGint-122 kcal/mol
Surface area61420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.710, 126.083, 249.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E
14B
24D
15B
25F
16D
26F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA10 - 3284 - 322
21ARGARGCB10 - 3284 - 322
12ARGARGAA10 - 3284 - 322
22ARGARGEC10 - 3284 - 322
13PROPROCB10 - 3314 - 325
23PROPROEC10 - 3314 - 325
14SERSERBD1 - 1741 - 174
24SERSERDE1 - 1741 - 174
15TYRTYRBD1 - 1411 - 141
25TYRTYRFF1 - 1411 - 141
16TYRTYRDE1 - 1411 - 141
26TYRTYRFF1 - 1411 - 141

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Hemagglutinin


Mass: 37948.020 Da / Num. of mol.: 3 / Fragment: N-terminal domain (UNP residues 17-337)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Vietnam/4/2003(H5N1))
Strain: A/chicken/Vietnam/4/2003(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q1KHJ8
#2: Protein Hemagglutinin


Mass: 20881.104 Da / Num. of mol.: 3 / Fragment: C-terminal domain (UNP residues 347-521)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Vietnam/30/2003(H5N1))
Strain: A/chicken/Vietnam/30/2003(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q1KHK7
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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
#4: Chemical ChemComp-R3P / 2,6-dichloro-N-[1-(propan-2-yl)piperidin-4-yl]benzamide


Mass: 315.238 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H20Cl2N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.24 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, pH 8.5, 20% PEG6000, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→29.47 Å / Num. obs: 110799 / % possible obs: 94.1 % / Redundancy: 5.49 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.092 / Net I/σ(I): 12.28
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.35 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 17093 / CC1/2: 0.755 / Rrim(I) all: 0.714 / % possible all: 91.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FKO

2fko


Resolution: 2.2→29.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.141 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 5426 4.9 %RANDOM
Rwork0.208 ---
obs0.2102 104199 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.13 Å2 / Biso mean: 49.644 Å2 / Biso min: 18.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2--1.37 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 2.2→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11616 0 172 435 12223
Biso mean--93.12 45.19 -
Num. residues----1454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312106
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710747
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.66216412
X-RAY DIFFRACTIONr_angle_other_deg1.2361.59825103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02151456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36723.807662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.821152069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.681556
X-RAY DIFFRACTIONr_chiral_restr0.0670.21561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213559
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022476
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A97780.07
12C97780.07
21A97780.06
22E97780.06
31C98780.07
32E98780.07
41B52970.08
42D52970.08
51B41560.07
52F41560.07
61D41890.06
62F41890.06
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 372 -
Rwork0.343 7266 -
all-7638 -
obs--88.99 %

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