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Basic information

Entry
Database: PDB / ID: 6lks
TitleEffects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Zinc induced the oligomerization / viral membrane protein / pH induced conformational change
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 / metal ion binding / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsSeok, J. / Kim, K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2010-0029242 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2020
Title: Divalent cation-induced conformational changes of influenza virus hemagglutinin.
Authors: Seok, J.H. / Kim, H. / Lee, D.B. / An, J.S. / Kim, E.J. / Lee, J.H. / Chung, M.S. / Kim, K.H.
History
DepositionDec 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,73246
Polymers345,00812
Non-polymers14,72434
Water7,710428
1
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,63824
Polymers172,5046
Non-polymers8,13418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,09322
Polymers172,5046
Non-polymers6,58916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.710, 124.270, 214.530
Angle α, β, γ (deg.)90.000, 102.909, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62
13
23
33
43
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and resid 3 through 322)A3 - 321
221(chain 'C' and resid 3 through 322)C3 - 321
331(chain 'E' and resid 3 through 322)E3 - 321
441chain 'G'G3 - 321
551chain 'I'I3 - 321
661(chain 'K' and resid 3 through 322)K3 - 321
172chain 'B'B1 - 164
282chain 'D'D1 - 164
392chain 'F'F1 - 164
4102chain 'H'H1 - 164
5112chain 'J'J1 - 164
6122chain 'L'L1 - 164
1133(chain 'a' and (resid 3 through 6 or resid 11 or resid 15 or resid 18))a3
1143(chain 'a' and (resid 3 through 6 or resid 11 or resid 15 or resid 18))a6
1153(chain 'a' and (resid 3 through 6 or resid 11 or resid 15 or resid 18))a11
1163(chain 'a' and (resid 3 through 6 or resid 11 or resid 15 or resid 18))a15
1173(chain 'a' and (resid 3 through 6 or resid 11 or resid 15 or resid 18))a18
2183(chain 'e' and (resid 6 through 7 or resid 12 or resid 16 or resid 18))e6 - 7
2193(chain 'e' and (resid 6 through 7 or resid 12 or resid 16 or resid 18))e12
2203(chain 'e' and (resid 6 through 7 or resid 12 or resid 16 or resid 18))e16
2213(chain 'e' and (resid 6 through 7 or resid 12 or resid 16 or resid 18))e18
3223(chain 'g' and (resid 1 through 3 or resid 10 or resid 14 or resid 16))g1
3233(chain 'g' and (resid 1 through 3 or resid 10 or resid 14 or resid 16))g3
3243(chain 'g' and (resid 1 through 3 or resid 10 or resid 14 or resid 16))g10
3253(chain 'g' and (resid 1 through 3 or resid 10 or resid 14 or resid 16))g14
3263(chain 'g' and (resid 1 through 3 or resid 10 or resid 14 or resid 16))g16
4273(chain 'k' and (resid 6 through 7 or resid 12 or resid 16 or resid 18))k6 - 7
4283(chain 'k' and (resid 6 through 7 or resid 12 or resid 16 or resid 18))k12
4293(chain 'k' and (resid 6 through 7 or resid 12 or resid 16 or resid 18))k16
4303(chain 'k' and (resid 6 through 7 or resid 12 or resid 16 or resid 18))k18
1314(chain 'c' and (resid 6 through 8 or resid 10 or resid 14))c6 - 8
1324(chain 'c' and (resid 6 through 8 or resid 10 or resid 14))c10
1334(chain 'c' and (resid 6 through 8 or resid 10 or resid 14))c14
2344(chain 'i' and (resid 6 through 8 or resid 10 or resid 15))i6 - 8
2354(chain 'i' and (resid 6 through 8 or resid 10 or resid 15))i10
2364(chain 'i' and (resid 6 through 8 or resid 10 or resid 15))i15

NCS ensembles :
ID
1
2
3
4

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Components

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Hemagglutinin ... , 2 types, 12 molecules KACEGILBDFHJ

#1: Protein
Hemagglutinin HA1 chain


Mass: 36662.137 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Thailand/CU44/2006(H1N1))
Gene: HA / Plasmid: pFastBac / Cell (production host): Bac to Bac / Cell line (production host): Hi-five / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A7LI25
#2: Protein
Hemagglutinin HA2 chain


Mass: 20839.188 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Thailand/CU44/2006(H1N1))
Gene: HA / Plasmid: pFastBac / Cell line (production host): Hi-five / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A7LI25

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Sugars , 5 types, 31 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 951.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+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.: 6
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: 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.: 1
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
#7: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 2 types, 431 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 4.28 Å3/Da / Density % sol: 71.27 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG 2000, Tris, DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.24→48.75 Å / Num. obs: 172506 / % possible obs: 99.91 % / Redundancy: 13.3 % / Biso Wilson estimate: 54.83 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rpim(I) all: 0.07844 / Rrim(I) all: 0.2875 / Net I/σ(I): 7.73
Reflection shellResolution: 3.24→3.356 Å / Mean I/σ(I) obs: 3.23 / Num. unique obs: 8830 / CC1/2: 0.92 / CC star: 0.979 / Rpim(I) all: 0.2064 / Rrim(I) all: 0.728 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCdata collection
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EDB

4edb


Resolution: 3.24→48.75 Å / SU ML: 0.4239 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.2345
RfactorNum. reflection% reflection
Rfree0.2948 3926 2.28 %
Rwork0.2654 --
obs0.2661 172506 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 74.73 Å2
Refinement stepCycle: LAST / Resolution: 3.24→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23024 0 961 428 24413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012824540
X-RAY DIFFRACTIONf_angle_d1.670733266
X-RAY DIFFRACTIONf_chiral_restr0.0883762
X-RAY DIFFRACTIONf_plane_restr0.01237136
X-RAY DIFFRACTIONf_dihedral_angle_d15.08333678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.280.33791430.32046163X-RAY DIFFRACTION99.97
3.28-3.320.36271420.30795984X-RAY DIFFRACTION99.98
3.32-3.360.34491410.30256081X-RAY DIFFRACTION100
3.36-3.410.32851370.30315893X-RAY DIFFRACTION99.98
3.41-3.460.31511410.30216066X-RAY DIFFRACTION100
3.46-3.510.28511350.28895949X-RAY DIFFRACTION99.89
3.51-3.570.32731430.26246080X-RAY DIFFRACTION99.9
3.57-3.620.31271360.26675959X-RAY DIFFRACTION99.95
3.62-3.690.29411400.27216041X-RAY DIFFRACTION100
3.69-3.750.31471430.27796081X-RAY DIFFRACTION100
3.75-3.830.33931400.28086009X-RAY DIFFRACTION100
3.83-3.90.36011440.27796060X-RAY DIFFRACTION99.95
3.9-3.990.28561400.2676012X-RAY DIFFRACTION100
3.99-4.080.27821380.25695926X-RAY DIFFRACTION99.98
4.08-4.180.27441410.26176097X-RAY DIFFRACTION99.97
4.18-4.30.30341400.25956018X-RAY DIFFRACTION99.74
4.3-4.420.29111400.25725988X-RAY DIFFRACTION99.98
4.42-4.570.28381370.24846035X-RAY DIFFRACTION99.95
4.57-4.730.22941410.24825959X-RAY DIFFRACTION99.87
4.73-4.920.27631440.23026083X-RAY DIFFRACTION100
4.92-5.140.29691400.24046031X-RAY DIFFRACTION99.98
5.14-5.410.2511380.24496043X-RAY DIFFRACTION99.92
5.41-5.750.2971390.23365957X-RAY DIFFRACTION99.97
5.75-6.190.24191430.24836057X-RAY DIFFRACTION99.95
6.19-6.820.27091390.25065972X-RAY DIFFRACTION99.92
6.82-7.80.30441420.27056073X-RAY DIFFRACTION99.76
7.8-9.810.27261410.25175988X-RAY DIFFRACTION99.95
9.81-48.750.31161380.28755975X-RAY DIFFRACTION99.22

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