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- PDB-4n5y: Crystal structure of H5 hemagglutinin mutant (N158D, N224K and Q2... -

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Basic information

Entry
Database: PDB / ID: 4n5y
TitleCrystal structure of H5 hemagglutinin mutant (N158D, N224K and Q226L) from the influenza virus A/Viet Nam/1203/2004 (H5N1)
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / H5N1 / Influenza Virus / hemagglutinin / Ferret transmissible
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 / identical protein binding
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 / Phaser / Resolution: 3.1615 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2014
Title: Hemagglutinin Receptor Specificity and Structural Analyses of Respiratory Droplet-Transmissible H5N1 Viruses.
Authors: de Vries, R.P. / Zhu, X. / McBride, R. / Rigter, A. / Hanson, A. / Zhong, G. / Hatta, M. / Xu, R. / Yu, W. / Kawaoka, Y. / de Haan, C.A. / Wilson, I.A. / Paulson, J.C.
History
DepositionOct 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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 / _chem_comp.name / _chem_comp.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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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 HA1 chain
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
G: Hemagglutinin HA1 chain
I: Hemagglutinin HA1 chain
K: Hemagglutinin HA1 chain
M: Hemagglutinin HA1 chain
O: Hemagglutinin HA1 chain
Q: Hemagglutinin HA1 chain
S: Hemagglutinin HA1 chain
U: Hemagglutinin HA1 chain
W: Hemagglutinin HA1 chain
Y: Hemagglutinin HA1 chain
a: Hemagglutinin HA1 chain
c: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
D: Hemagglutinin HA2 chain
F: Hemagglutinin HA2 chain
H: Hemagglutinin HA2 chain
J: Hemagglutinin HA2 chain
L: Hemagglutinin HA2 chain
N: Hemagglutinin HA2 chain
P: Hemagglutinin HA2 chain
R: Hemagglutinin HA2 chain
T: Hemagglutinin HA2 chain
V: Hemagglutinin HA2 chain
X: Hemagglutinin HA2 chain
Z: Hemagglutinin HA2 chain
b: Hemagglutinin HA2 chain
d: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)895,69159
Polymers882,45330
Non-polymers13,23729
Water0
1
A: Hemagglutinin HA1 chain
G: Hemagglutinin HA1 chain
I: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
H: Hemagglutinin HA2 chain
J: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,52312
Polymers176,4916
Non-polymers3,0336
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28110 Å2
ΔGint-130 kcal/mol
Surface area62920 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
K: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
F: Hemagglutinin HA2 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,89611
Polymers176,4916
Non-polymers2,4055
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28360 Å2
ΔGint-135 kcal/mol
Surface area63320 Å2
MethodPISA
3
M: Hemagglutinin HA1 chain
O: Hemagglutinin HA1 chain
Q: Hemagglutinin HA1 chain
N: Hemagglutinin HA2 chain
P: Hemagglutinin HA2 chain
R: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,90713
Polymers176,4916
Non-polymers3,4167
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28090 Å2
ΔGint-135 kcal/mol
Surface area63320 Å2
MethodPISA
4
S: Hemagglutinin HA1 chain
U: Hemagglutinin HA1 chain
W: Hemagglutinin HA1 chain
T: Hemagglutinin HA2 chain
V: Hemagglutinin HA2 chain
X: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,36112
Polymers176,4916
Non-polymers2,8716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28200 Å2
ΔGint-124 kcal/mol
Surface area63500 Å2
MethodPISA
5
Y: Hemagglutinin HA1 chain
a: Hemagglutinin HA1 chain
c: Hemagglutinin HA1 chain
Z: Hemagglutinin HA2 chain
b: Hemagglutinin HA2 chain
d: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,00311
Polymers176,4916
Non-polymers1,5125
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28910 Å2
ΔGint-130 kcal/mol
Surface area63280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.915, 118.105, 273.799
Angle α, β, γ (deg.)91.50, 90.18, 119.87
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Hemagglutinin ... , 2 types, 30 molecules ACEGIKMOQSUWYacBDFHJLNPRTVXZbd

#1: Protein
Hemagglutinin HA1 chain


Mass: 37949.113 Da / Num. of mol.: 15 / Fragment: receptor binding domain, HA1 / Mutation: N158D, N224K, Q226L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/VIET NAM/1203/2004 / Gene: HA / Plasmid: PFASTBAC-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6DQ33
#2: Protein
Hemagglutinin HA2 chain


Mass: 20881.104 Da / Num. of mol.: 15 / Fragment: membrane fusion domain, HA2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/VIET NAM/1203/2004 / Gene: HA / Plasmid: PFASTBAC-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6DQ33

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Sugars , 4 types, 29 molecules

#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 13
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
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 5
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.2 KF, 22% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.05876 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05876 Å / Relative weight: 1
ReflectionResolution: 3.1615→50 Å / Num. obs: 199766 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.13 / Net I/σ(I): 7.1
Reflection shellResolution: 3.1615→3.27 Å / % possible all: 83.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Phaser
Starting model: PDB ENTRY 3GBM

3gbm


Resolution: 3.1615→45.283 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 9981 5 %RANDPM
Rwork0.2126 ---
obs0.215 199509 91.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1615→45.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60015 0 874 0 60889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01262596
X-RAY DIFFRACTIONf_angle_d1.55584676
X-RAY DIFFRACTIONf_dihedral_angle_d19.41823365
X-RAY DIFFRACTIONf_chiral_restr0.0699153
X-RAY DIFFRACTIONf_plane_restr0.00810979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1615-3.19740.3222780.30491412X-RAY DIFFRACTION20
3.1974-3.2350.36452880.32355323X-RAY DIFFRACTION79
3.235-3.27440.35312970.32366053X-RAY DIFFRACTION85
3.2744-3.31590.38033040.32136018X-RAY DIFFRACTION89
3.3159-3.35950.3373370.29636135X-RAY DIFFRACTION87
3.3595-3.40550.34443130.30616141X-RAY DIFFRACTION89
3.4055-3.45410.33172820.28826216X-RAY DIFFRACTION89
3.4541-3.50570.34843130.29776115X-RAY DIFFRACTION88
3.5057-3.56040.29823170.26226310X-RAY DIFFRACTION90
3.5604-3.61880.28363250.25226277X-RAY DIFFRACTION91
3.6188-3.68110.28363250.25366376X-RAY DIFFRACTION90
3.6811-3.7480.31193040.24746096X-RAY DIFFRACTION89
3.748-3.82010.28033830.23616473X-RAY DIFFRACTION93
3.8201-3.8980.2973630.23326435X-RAY DIFFRACTION94
3.898-3.98270.30753550.24276272X-RAY DIFFRACTION91
3.9827-4.07530.25313770.19396697X-RAY DIFFRACTION95
4.0753-4.17720.25133300.19146614X-RAY DIFFRACTION96
4.1772-4.290.23773670.17916675X-RAY DIFFRACTION97
4.29-4.41620.22193680.16626757X-RAY DIFFRACTION98
4.4162-4.55860.19883850.17056795X-RAY DIFFRACTION98
4.5586-4.72130.20494080.16566795X-RAY DIFFRACTION98
4.7213-4.91020.21443270.16356847X-RAY DIFFRACTION99
4.9102-5.13330.23083760.1736838X-RAY DIFFRACTION98
5.1333-5.40360.24513780.17246816X-RAY DIFFRACTION99
5.4036-5.74150.22163850.16636767X-RAY DIFFRACTION99
5.7415-6.18380.23253390.18696931X-RAY DIFFRACTION99
6.1838-6.80420.25353340.18956855X-RAY DIFFRACTION99
6.8042-7.78450.2463680.19536852X-RAY DIFFRACTION99
7.7845-9.79130.24763260.18626908X-RAY DIFFRACTION99
9.7913-45.28790.26163290.22926729X-RAY DIFFRACTION97

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