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- PDB-4dj6: Structure of the hemagglutinin from a highly pathogenic H7N7 infl... -

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Basic information

Entry
Database: PDB / ID: 4dj6
TitleStructure of the hemagglutinin 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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_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)171,79018
Polymers168,9326
Non-polymers2,85812
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35150 Å2
ΔGint-119 kcal/mol
Surface area59250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.949, 116.573, 117.320
Angle α, β, γ (deg.)90.00, 124.92, 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 8
Details: 20 % PEG 8000 and 1 M lithium chloride, microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 30, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 126587 / Num. obs: 12472 / % possible obs: 99 % / Observed criterion σ(F): 13.6 / Observed criterion σ(I): 2.6 / Redundancy: 3.2 % / Rsym value: 0.141
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.8 % / Rsym value: 0.498 / % possible all: 98.2

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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: 2.61→49.85 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.848 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.453 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23571 3421 5.1 %RANDOM
Rwork0.20347 ---
obs0.20516 12472 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.561 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å2-2.54 Å2
2--2.01 Å2-0 Å2
3----4.04 Å2
Refinement stepCycle: LAST / Resolution: 2.61→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11407 0 182 215 11804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111816
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.95315983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.45251453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93124.636591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.474151985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6641582
X-RAY DIFFRACTIONr_chiral_restr0.0850.21743
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219085
X-RAY DIFFRACTIONr_mcbond_it0.94337195
X-RAY DIFFRACTIONr_mcangle_it1.948511560
X-RAY DIFFRACTIONr_scbond_it4.03784621
X-RAY DIFFRACTIONr_scangle_it6.956114423
LS refinement shellResolution: 2.606→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 220 -
Rwork0.316 4278 -
obs--89.25 %
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)
10.69390.02650.56890.81960.44093.10580.0448-0.0696-0.1083-0.0564-0.0523-0.11150.17710.00110.00750.04220.0184-0.01510.03250.03350.12845.25063.0836-9.8987
20.227-0.20020.30220.4576-0.81046.6478-0.1036-0.20730.09930.22510.0086-0.2266-0.00140.31970.0950.26830.0457-0.16340.4218-0.00950.138444.059310.803440.489
30.8055-0.1072-0.02560.7443-0.60863.02590.020.0508-0.05680.0588-0.05530.1426-0.0731-0.12150.03520.0087-0.00120.02160.0588-0.00840.121215.337214.6891-9.7131
40.6366-0.0468-1.00780.07760.10917.2995-0.0698-0.2509-0.29640.1363-0.08710.03590.219-0.1810.15680.3361-0.09510.090.34090.15170.171922.725512.105441.0119
50.8880.072-0.68560.71710.34183.162-0.0974-0.01280.1384-0.00830.0492-0.0247-0.10040.13860.04820.0405-0.0201-0.03110.0275-0.01990.118340.290134.868-9.7501
60.25310.20750.51530.41170.77926.9305-0.0622-0.19270.16270.2168-0.12790.2217-0.2167-0.11650.19010.38560.0170.08870.3002-0.14320.153234.546829.97940.4076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 317
2X-RAY DIFFRACTION1A401 - 404
3X-RAY DIFFRACTION1A501 - 559
4X-RAY DIFFRACTION2B1 - 170
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION2B301 - 312
7X-RAY DIFFRACTION3C1 - 317
8X-RAY DIFFRACTION3C401 - 403
9X-RAY DIFFRACTION3C501 - 559
10X-RAY DIFFRACTION4D1 - 171
11X-RAY DIFFRACTION4D201
12X-RAY DIFFRACTION4D301 - 313
13X-RAY DIFFRACTION5E0 - 317
14X-RAY DIFFRACTION5E401 - 403
15X-RAY DIFFRACTION5E501 - 554
16X-RAY DIFFRACTION6F1 - 169
17X-RAY DIFFRACTION6F201
18X-RAY DIFFRACTION6F301 - 318

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