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- PDB-4dj8: Structure of the hemagglutinin complexed with 6SLN from a highly ... -

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Basic information

Entry
Database: PDB / ID: 4dj8
TitleStructure of the hemagglutinin complexed with 6SLN from a highly pathogenic H7N7 influenza virus
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / receptor binding / glycoprotein
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYang, H. / Carney, P.J. / Donis, R.O. / Stevens, J.
CitationJournal: J.Virol. / Year: 2012
Title: Structure and receptor complexes of the hemagglutinin from a highly pathogenic H7N7 influenza virus.
Authors: Yang, H. / Carney, P.J. / Donis, R.O. / Stevens, J.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)172,51521
Polymers168,9326
Non-polymers3,58215
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37100 Å2
ΔGint-159 kcal/mol
Surface area59230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.774, 117.603, 120.456
Angle α, β, γ (deg.)90.00, 124.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin /


Mass: 35878.391 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 26-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Netherlands/219/2003(H7N7))
Production host: trichoplusia ni (cabbage looper) / References: UniProt: Q6VMK1
#2: Protein Hemagglutinin /


Mass: 20432.391 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 349-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Netherlands/219/2003(H7N7))
Production host: trichoplusia ni (cabbage looper) / References: UniProt: Q6VMK1
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8
Details: 20 % PEG 8000 and 1 M lithium chloride, microbatch under oil, temperature 298K, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 58241 / Num. obs: 54989 / % possible obs: 99.9 % / Observed criterion σ(F): 23.7 / Observed criterion σ(I): 3.5 / Redundancy: 3.8 % / Rsym value: 0.067
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.7 % / Rsym value: 0.369 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.23 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 24.468 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.655 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23494 2934 5.1 %RANDOM
Rwork0.19016 ---
obs0.19251 54988 99.89 %-
all-96681 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å2-0.2 Å2
2--0.07 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11407 0 228 103 11738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02211871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.95716059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.32951455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83524.587593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.709151982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0141584
X-RAY DIFFRACTIONr_chiral_restr0.1320.21753
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219122
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.32837196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.83511560
X-RAY DIFFRACTIONr_scbond_it5.48384705
X-RAY DIFFRACTIONr_scangle_it9.292114538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 184 -
Rwork0.309 3995 -
obs--99.83 %
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)
10.81550.2258-0.07880.55070.08470.08110.0923-0.18450.02390.1106-0.11320.00050.06180.07610.02090.09440.0332-0.00190.16680.01440.196752.4926-12.956760.1464
20.3204-0.0621-0.20790.277-0.16712.8881-0.02760.1976-0.1357-0.1644-0.0446-0.07790.1260.09760.07220.21280.01640.08660.2703-0.08630.102645.2114-14.67358.7543
30.7538-0.25050.08930.5868-0.05250.033-0.1028-0.207-0.02930.05210.07980.0157-0.0643-0.01850.0230.15050.0156-0.00660.07730.00660.197528.23298.586960.103
40.25920.01970.27190.5115-0.33813.3171-0.02860.16340.1398-0.2546-0.0374-0.0831-0.05910.06860.0660.2560.01150.03340.20720.12120.103833.25113.09288.4974
50.34020.0295-0.00960.80180.11630.0504-0.01890.01370.00350.2034-0.0054-0.02110.0608-0.06010.02430.0986-0.05250.00710.116-0.00330.202721.609-23.149359.8917
60.40870.09070.09880.32390.41853.1298-0.07260.19020.016-0.19430.01210.1497-0.0035-0.05610.06040.2348-0.0281-0.10290.2233-0.02520.081523.7776-16.18419.0006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 316
2X-RAY DIFFRACTION1A401 - 404
3X-RAY DIFFRACTION1A501 - 522
4X-RAY DIFFRACTION2B1 - 170
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION2B301 - 314
7X-RAY DIFFRACTION3C1 - 316
8X-RAY DIFFRACTION3C401 - 404
9X-RAY DIFFRACTION3C501 - 525
10X-RAY DIFFRACTION4D1 - 171
11X-RAY DIFFRACTION4D201
12X-RAY DIFFRACTION4D301 - 311
13X-RAY DIFFRACTION5E0 - 316
14X-RAY DIFFRACTION5E401 - 404
15X-RAY DIFFRACTION5E501 - 518
16X-RAY DIFFRACTION6F1 - 169
17X-RAY DIFFRACTION6F201
18X-RAY DIFFRACTION6F301 - 313

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