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- PDB-6v48: The crystal structure of hemagglutinin from A/mallard/Gurjev/263/... -

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Basic information

Entry
Database: PDB / ID: 6v48
TitleThe crystal structure of hemagglutinin from A/mallard/Gurjev/263/1982 (H14N5)
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Influenza / avian / H14
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 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsYang, H. / Stevens, J.
CitationJournal: Heliyon / Year: 2020
Title: Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins
Authors: Yang, H. / Carney, P.J. / Chang, J. / Stevens, J.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: 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 / 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 16, 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
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
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,57530
Polymers348,15512
Non-polymers6,42018
Water00
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,28715
Polymers174,0776
Non-polymers3,2109
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35160 Å2
ΔGint-76 kcal/mol
Surface area58430 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
hetero molecules

G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
hetero molecules

I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,28715
Polymers174,0776
Non-polymers3,2109
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area35160 Å2
ΔGint-78 kcal/mol
Surface area58420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.665, 100.974, 236.075
Angle α, β, γ (deg.)90.000, 103.930, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
41chain G
51chain I
61chain K
12chain B
22chain D
32chain F
42chain H
52chain J
62chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLYchain AAA9 - 32713 - 331
21GLYGLYGLYGLYchain CCC9 - 32713 - 331
31GLYGLYGLYGLYchain EEE9 - 32713 - 331
41GLYGLYGLYGLYchain GGG9 - 32713 - 331
51GLYGLYGLYGLYchain III9 - 32713 - 331
61GLYGLYGLYGLYchain KKK9 - 32713 - 331
12ALAALALYSLYSchain BBB5 - 1725 - 172
22ALAALALYSLYSchain DDD5 - 1725 - 172
32ALAALALYSLYSchain FFF5 - 1725 - 172
42ALAALALYSLYSchain HHH5 - 1725 - 172
52ALAALALYSLYSchain JJJ5 - 1725 - 172
62ALAALALYSLYSchain LLL5 - 1725 - 172

NCS ensembles :
ID
1
2

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Components

#1: Protein
Hemagglutinin HA1 chain


Mass: 36407.820 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Mallard/Gurjev/263/1982 H14N5)
Strain: A/Mallard/Gurjev/263/1982 H14N5 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P26136
#2: Protein
Hemagglutinin HA2 chain


Mass: 21617.939 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Mallard/Gurjev/263/1982 H14N5)
Strain: A/Mallard/Gurjev/263/1982 H14N5 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P26136
#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.: 12
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: 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.: 6
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
Has ligand of interestN
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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2M Sodium cacodylate trihydrate pH5.5, 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 79098 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.116 / Net I/σ(I): 7.7
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 3949 / Rsym value: 0.56

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYJ

3eyj


Resolution: 3.004→45.11 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.05
RfactorNum. reflection% reflection
Rfree0.2602 3949 4.99 %
Rwork0.2242 --
obs0.226 79098 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 219.19 Å2 / Biso mean: 60.2983 Å2 / Biso min: 1.09 Å2
Refinement stepCycle: final / Resolution: 3.004→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22902 0 420 0 23322
Biso mean--80.31 --
Num. residues----2922
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5898X-RAY DIFFRACTION0.827TORSIONAL
12C5898X-RAY DIFFRACTION0.827TORSIONAL
13E5898X-RAY DIFFRACTION0.827TORSIONAL
14G5898X-RAY DIFFRACTION0.827TORSIONAL
15I5898X-RAY DIFFRACTION0.827TORSIONAL
16K5898X-RAY DIFFRACTION0.827TORSIONAL
21B3138X-RAY DIFFRACTION0.827TORSIONAL
22D3138X-RAY DIFFRACTION0.827TORSIONAL
23F3138X-RAY DIFFRACTION0.827TORSIONAL
24H3138X-RAY DIFFRACTION0.827TORSIONAL
25J3138X-RAY DIFFRACTION0.827TORSIONAL
26L3138X-RAY DIFFRACTION0.827TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.004-3.04020.33341080.3062216880
3.0402-3.07870.33061280.28582677100
3.0787-3.11920.30831480.28412691100
3.1192-3.16190.372990.29362741100
3.1619-3.20710.35451190.28022683100
3.2071-3.25490.31831340.25032789100
3.2549-3.30580.27951380.25852614100
3.3058-3.360.28781650.25982728100
3.36-3.41790.31951360.26342636100
3.4179-3.480.28761590.24932730100
3.48-3.54690.28841280.24482623100
3.5469-3.61930.26921540.2242734100
3.6193-3.69790.2331690.21822661100
3.6979-3.78390.20381310.21892694100
3.7839-3.87850.24041220.2012788100
3.8785-3.98330.25311510.21042632100
3.9833-4.10040.26261390.20622678100
4.1004-4.23270.20581660.19992727100
4.2327-4.38390.21791410.1862731100
4.3839-4.55920.24911550.19312647100
4.5592-4.76650.24441430.17832717100
4.7665-5.01750.24021420.18382724100
5.0175-5.33140.1861450.1852698100
5.3314-5.74230.25971680.20392656100
5.7423-6.31880.25881310.21282784100
6.3188-7.22990.26591560.21692737100
7.2299-9.09660.24151410.22122732100
8-9.10.27981330.246272996
Refinement TLS params.Method: refined / Origin x: 14.5013 Å / Origin y: -0.8205 Å / Origin z: 53.148 Å
111213212223313233
T-0.0007 Å20.0066 Å20.0026 Å2-0.0599 Å20.0025 Å2--0.0419 Å2
L0.0754 °20.019 °2-0.0092 °2-0.1252 °2-0.0309 °2--0.0244 °2
S0.0171 Å °-0.0783 Å °0.0117 Å °0.0802 Å °-0.0103 Å °0.0455 Å °-0.0231 Å °0.0248 Å °0.0015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 327
2X-RAY DIFFRACTION1allA501 - 602
3X-RAY DIFFRACTION1allB5 - 172
4X-RAY DIFFRACTION1allB201 - 202
5X-RAY DIFFRACTION1allC9 - 327
6X-RAY DIFFRACTION1allC501 - 602
7X-RAY DIFFRACTION1allD5 - 172
8X-RAY DIFFRACTION1allD201 - 202
9X-RAY DIFFRACTION1allE9 - 327
10X-RAY DIFFRACTION1allE501 - 602
11X-RAY DIFFRACTION1allF5 - 172
12X-RAY DIFFRACTION1allF201 - 202
13X-RAY DIFFRACTION1allG9 - 327
14X-RAY DIFFRACTION1allG501 - 602
15X-RAY DIFFRACTION1allH5 - 172
16X-RAY DIFFRACTION1allH201 - 202
17X-RAY DIFFRACTION1allI9 - 327
18X-RAY DIFFRACTION1allI501 - 602
19X-RAY DIFFRACTION1allJ5 - 172
20X-RAY DIFFRACTION1allJ201 - 202
21X-RAY DIFFRACTION1allK9 - 327
22X-RAY DIFFRACTION1allK501 - 602
23X-RAY DIFFRACTION1allL5 - 172
24X-RAY DIFFRACTION1allL201 - 202

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