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- PDB-4jug: Crystal structure of 1918 pandemic influenza virus hemagglutinin ... -

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Basic information

Entry
Database: PDB / ID: 4jug
TitleCrystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / virus attachment / membrane fusion
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / 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: 2.7 Å
AuthorsZhang, W. / Shi, Y. / Qi, J. / Gao, F. / Li, Q. / Fan, Z. / Yan, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2013
Title: Molecular basis of the receptor binding specificity switch of the hemagglutinins from both the 1918 and 2009 pandemic influenza A viruses by a D225G substitution
Authors: Zhang, W. / Shi, Y. / Qi, J. / Gao, F. / Li, Q. / Fan, Z. / Yan, J. / Gao, G.F.
History
DepositionMar 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 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 / 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_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Nov 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,68320
Polymers330,96312
Non-polymers3,7198
Water3,729207
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,34110
Polymers165,4826
Non-polymers1,8604
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31060 Å2
ΔGint-118 kcal/mol
Surface area59200 Å2
MethodPISA
2
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,34110
Polymers165,4826
Non-polymers1,8604
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31010 Å2
ΔGint-119 kcal/mol
Surface area59340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.856, 120.856, 235.724
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: 35710.066 Da / Num. of mol.: 6 / Fragment: Hemagglutinin HA1 chain, UNP residues 18-339 / Mutation: D225G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/18 (H1N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9WFX3
#2: Protein
Hemagglutinin


Mass: 19450.465 Da / Num. of mol.: 6 / Fragment: Hemagglutinin HA2 chain, UNP residues 345-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/18 (H1N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9WFX3
#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.: 6
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 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.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 6000, 5% MPD, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 104397 / Num. obs: 104397 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 89.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RUZ

1ruz


Resolution: 2.7→47.901 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7625 / SU ML: 0.44 / σ(F): 0.11 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 4892 5.03 %
Rwork0.2074 --
obs0.2104 97310 91.95 %
all-97310 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.028 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 172.88 Å2 / Biso mean: 63.6483 Å2 / Biso min: 21.99 Å2
Baniso -1Baniso -2Baniso -3
1-9.9131 Å2-0 Å2-0 Å2
2--9.9131 Å20 Å2
3----19.8263 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23158 0 246 207 23611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424004
X-RAY DIFFRACTIONf_angle_d0.82632536
X-RAY DIFFRACTIONf_chiral_restr0.063539
X-RAY DIFFRACTIONf_plane_restr0.0034201
X-RAY DIFFRACTIONf_dihedral_angle_d19.458592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6999-2.73060.39471240.32462253237767
2.7306-2.76270.35421390.31512421256072
2.7627-2.79640.40821180.29142616273478
2.7964-2.83180.38181310.27652730286181
2.8318-2.86910.36521490.26722809295884
2.8691-2.90840.3241630.25612916307987
2.9084-2.94990.32671600.26982932309287
2.9499-2.99390.3571660.26852909307588
2.9939-3.04070.34231630.24933016317989
3.0407-3.09050.31191500.24433002315290
3.0905-3.14380.33421510.25273068321992
3.1438-3.2010.31671970.24163121331893
3.201-3.26250.33621540.23693217337195
3.2625-3.32910.30891640.23153102326694
3.3291-3.40150.31011580.233186334495
3.4015-3.48060.30241890.21843231342096
3.4806-3.56760.25291750.21233212338797
3.5676-3.6640.27571840.20253269345397
3.664-3.77180.24791480.19953265341397
3.7718-3.89350.29061730.20213309348298
3.8935-4.03260.22211700.18063223339397
4.0326-4.19390.23641810.16353258343998
4.1939-4.38470.19041830.1593262344598
4.3847-4.61570.21161810.15933296347798
4.6157-4.90460.21851800.16033319349999
4.9046-5.28290.19221700.16433285345599
5.2829-5.81370.25471680.1833307347599
5.8137-6.6530.27941890.19833266345598
6.653-8.37480.21431580.1813349350799
8.3748-47.90830.20551560.18353269342597
Refinement TLS params.Method: refined / Origin x: 0.8867 Å / Origin y: 34.988 Å / Origin z: -25.5766 Å
111213212223313233
T0.1995 Å20.0225 Å2-0.0109 Å2-0.2346 Å2-0.005 Å2--0.2174 Å2
L0.0628 °20.0086 °2-0.1273 °2-0.004 °20.0104 °2--0.277 °2
S-0.0097 Å °-0.0133 Å °-0.0113 Å °0.0012 Å °-0.0274 Å °0.0064 Å °0.048 Å °-0.0113 Å °0.0403 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA5 - 327
2X-RAY DIFFRACTION1ALLB501 - 670
3X-RAY DIFFRACTION1ALLC5 - 327
4X-RAY DIFFRACTION1ALLD501 - 669
5X-RAY DIFFRACTION1ALLE5 - 327
6X-RAY DIFFRACTION1ALLF501 - 665
7X-RAY DIFFRACTION1ALLG5 - 327
8X-RAY DIFFRACTION1ALLH501 - 670
9X-RAY DIFFRACTION1ALLI5 - 327
10X-RAY DIFFRACTION1ALLJ501 - 667
11X-RAY DIFFRACTION1ALLK5 - 327
12X-RAY DIFFRACTION1ALLL501 - 665
13X-RAY DIFFRACTION1ALLA801 - 802
14X-RAY DIFFRACTION1ALLC801 - 802
15X-RAY DIFFRACTION1ALLD801 - 803
16X-RAY DIFFRACTION1ALLE801 - 802
17X-RAY DIFFRACTION1ALLG801 - 802
18X-RAY DIFFRACTION1ALLI801 - 802
19X-RAY DIFFRACTION1ALLJ801 - 803
20X-RAY DIFFRACTION1ALLK801 - 802
21X-RAY DIFFRACTION1ALLA901 - 916
22X-RAY DIFFRACTION1ALLB701 - 706
23X-RAY DIFFRACTION1ALLC901 - 935
24X-RAY DIFFRACTION1ALLD901 - 919
25X-RAY DIFFRACTION1ALLE901 - 918
26X-RAY DIFFRACTION1ALLF701 - 706
27X-RAY DIFFRACTION1ALLG901 - 914
28X-RAY DIFFRACTION1ALLH701 - 705
29X-RAY DIFFRACTION1ALLI901 - 945
30X-RAY DIFFRACTION1ALLJ901 - 924
31X-RAY DIFFRACTION1ALLK901 - 912
32X-RAY DIFFRACTION1ALLL701 - 707

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