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- PDB-4dj7: Structure of the hemagglutinin complexed with 3SLN from a highly ... -

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Basic information

Entry
Database: PDB / ID: 4dj7
TitleStructure of the hemagglutinin complexed with 3SLN 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
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 / entity_name_com / 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_molecule_features / 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)173,81421
Polymers168,9326
Non-polymers4,88215
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37570 Å2
ΔGint-113 kcal/mol
Surface area59580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.279, 115.723, 117.656
Angle α, β, γ (deg.)90.00, 124.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 6 molecules ACEBDF

#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

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Sugars , 3 types, 15 molecules

#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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: 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

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Non-polymers , 1 types, 30 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.33 Å3/Da / Density % sol: 63.06 %
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-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 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: 2.8→50 Å / Num. obs: 49829 / % possible obs: 97.8 % / Observed criterion σ(F): 24.5 / Observed criterion σ(I): 1.3 / Redundancy: 3.7 % / Rsym value: 0.087
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Rsym value: 0.693 / % possible all: 90.9

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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: 2.81→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 30.068 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 1.207 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24263 2681 5.1 %RANDOM
Rwork0.20745 ---
obs0.20922 49829 97.16 %-
all-88905 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.155 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å2-1.41 Å2
2---0.86 Å2-0 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11399 0 320 30 11749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111952
X-RAY DIFFRACTIONr_angle_refined_deg1.111.96716179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.42451452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47324.627590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.165151984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1661582
X-RAY DIFFRACTIONr_chiral_restr0.090.21790
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219119
X-RAY DIFFRACTIONr_mcbond_it1.09837190
X-RAY DIFFRACTIONr_mcangle_it2.08511552
X-RAY DIFFRACTIONr_scbond_it4.42584762
X-RAY DIFFRACTIONr_scangle_it7.552114627
LS refinement shellResolution: 2.81→2.883 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 161 -
Rwork0.342 3074 -
obs--81.24 %
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)
11.19410.28130.61371.23190.75323.70360.0845-0.3609-0.02820.2733-0.1251-0.17420.1119-0.02510.04060.0775-0.0195-0.05060.14390.01250.254751.8192-11.802458.6078
20.6592-0.0824-0.73270.2873-0.0147.0345-0.00030.2131-0.2511-0.1456-0.083-0.00570.2246-0.0810.08340.23170.04390.02780.1567-0.12170.136144.3577-14.317.5888
31.5984-0.0838-0.9771.01750.14444.0575-0.087-0.44670.19440.19760.08580.0779-0.04880.09340.00120.11960.0582-0.01880.1434-0.04030.271727.19968.832158.7111
40.5933-0.04770.35880.419-0.66777.6342-0.06280.20890.2387-0.2199-0.0627-0.14670.07840.18620.12550.299-0.02580.03430.11360.13390.179233.00693.69777.3315
51.0519-0.18630.21781.2849-0.64033.6241-0.0449-0.1952-0.11670.37440.04530.11340.0321-0.1126-0.00050.1799-0.0270.0150.06030.01270.253521.559-22.71658.3192
60.47310.14740.43130.6090.55347.4549-0.0640.22480.0691-0.19320.01220.304-0.1638-0.15010.05180.1629-0.0183-0.17010.23640.00170.214223.0687-15.14837.8613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 317
2X-RAY DIFFRACTION1A401 - 407
3X-RAY DIFFRACTION1A501 - 503
4X-RAY DIFFRACTION2B1 - 170
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION2B301 - 304
7X-RAY DIFFRACTION3C2 - 317
8X-RAY DIFFRACTION3C401 - 406
9X-RAY DIFFRACTION3C501 - 507
10X-RAY DIFFRACTION4D1 - 171
11X-RAY DIFFRACTION4D201
12X-RAY DIFFRACTION4D301 - 305
13X-RAY DIFFRACTION5E0 - 317
14X-RAY DIFFRACTION5E401 - 406
15X-RAY DIFFRACTION5E501 - 506
16X-RAY DIFFRACTION6F1 - 169
17X-RAY DIFFRACTION6F201
18X-RAY DIFFRACTION6F301 - 305

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