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- PDB-4lkg: The structure of hemagglutinin from a avian-origin H7N9 influenza... -

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Basic information

Entry
Database: PDB / ID: 4lkg
TitleThe structure of hemagglutinin from a avian-origin H7N9 influenza virus (A/Shanghai/1/2013) in complex with avian receptor analog 3'SLNLN
Components(hemagglutinin) x 2
KeywordsVIRAL PROTEIN / homotrimer / virus attachment / membrane fusion
Function / homology
Function and homology information


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
Similarity search - Function
Haemagglutinin, influenzavirus 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 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 / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å
AuthorsShi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. ...Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F.
CitationJournal: Science / Year: 2013
Title: Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses
Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / ...Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F.
History
DepositionJul 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / struct_asym / struct_conn / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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
C: hemagglutinin
D: hemagglutinin
E: hemagglutinin
F: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,64212
Polymers162,3616
Non-polymers2,2816
Water0
1
A: hemagglutinin
B: hemagglutinin
hetero molecules

A: hemagglutinin
B: hemagglutinin
hetero molecules

A: hemagglutinin
B: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,04812
Polymers162,3616
Non-polymers2,6876
Water0
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
Buried area36590 Å2
ΔGint-121 kcal/mol
Surface area55810 Å2
MethodPISA
2
C: hemagglutinin
D: hemagglutinin
hetero molecules

C: hemagglutinin
D: hemagglutinin
hetero molecules

C: hemagglutinin
D: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,43912
Polymers162,3616
Non-polymers2,0786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area35210 Å2
ΔGint-136 kcal/mol
Surface area56150 Å2
MethodPISA
3
E: hemagglutinin
F: hemagglutinin
hetero molecules

E: hemagglutinin
F: hemagglutinin
hetero molecules

E: hemagglutinin
F: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,43912
Polymers162,3616
Non-polymers2,0786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area35090 Å2
ΔGint-139 kcal/mol
Surface area56330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.764, 110.764, 133.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein hemagglutinin /


Mass: 34485.773 Da / Num. of mol.: 3 / Fragment: residues 1-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/SHANGHAI/1/2013 / Plasmid: pFastbac1 / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V5IRV0*PLUS
#2: Protein hemagglutinin /


Mass: 19634.502 Da / Num. of mol.: 3 / Fragment: residues 322-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/SHANGHAI/1/2013 / Plasmid: pFastbac1 / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V5IRU7*PLUS
#3: 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.: 1
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
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#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
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/SHANGHAI/1/2013 DOES ...THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/SHANGHAI/1/2013 DOES NOT CURRENTLY EXIST.

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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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M sodium citrate tribasic dehydrate, 18%(w/v) Polyethylene glycol 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.994→50 Å / Num. all: 36814 / Num. obs: 36748 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 72.73 Å2
Reflection shellResolution: 3→3.11 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DJ6

4dj6


Resolution: 2.994→42.586 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7631 / SU ML: 0.44 / σ(F): 1.97 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 1838 5 %RANDOM
Rwork0.2456 ---
all0.2472 36742 --
obs0.2472 36742 99.71 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.649 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso max: 336.49 Å2 / Biso mean: 100.5732 Å2 / Biso min: 33.74 Å2
Baniso -1Baniso -2Baniso -3
1-3.9463 Å20 Å2-0 Å2
2--3.9463 Å20 Å2
3----7.8926 Å2
Refinement stepCycle: LAST / Resolution: 2.994→42.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11379 0 152 0 11531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511763
X-RAY DIFFRACTIONf_angle_d0.89515868
X-RAY DIFFRACTIONf_chiral_restr0.191730
X-RAY DIFFRACTIONf_plane_restr0.0032089
X-RAY DIFFRACTIONf_dihedral_angle_d18.0594340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9937-3.07470.40141360.35142687282399
3.0747-3.16510.38241360.346427002836100
3.1651-3.26720.38751530.325926612814100
3.2672-3.3840.36941420.310927052847100
3.384-3.51940.34111300.285126542784100
3.5194-3.67950.30261200.260427112831100
3.6795-3.87340.27761610.248326922853100
3.8734-4.11580.25781490.223226992848100
4.1158-4.43330.26111410.202826942835100
4.4333-4.87890.21851310.19826712802100
4.8789-5.58350.23711460.214426912837100
5.5835-7.02950.27451480.242226712819100
7.0295-42.59050.24991450.24062668281399
Refinement TLS params.Method: refined / Origin x: 32.6107 Å / Origin y: -5.4955 Å / Origin z: 10.6598 Å
111213212223313233
T0.4532 Å20.0407 Å2-0.0716 Å2-0.3957 Å2-0.0243 Å2--0.3977 Å2
L0.3256 °2-0.0863 °2-0.2069 °2-0.0953 °20.075 °2---0.1084 °2
S-0.0154 Å °-0.0031 Å °0.0403 Å °-0.0488 Å °-0.0376 Å °-0.0266 Å °-0.1033 Å °-0.0856 Å °-0.0007 Å °
Refinement TLS groupSelection details: ALL

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