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- PDB-6p6p: Crystal structure of hemagglutinin from influenza virus A/Sichuan... -

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Basic information

Entry
Database: PDB / ID: 6p6p
TitleCrystal structure of hemagglutinin from influenza virus A/Sichuan/2/1987 (H3N2)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / virion membrane
Similarity search - Function
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: 2.31 Å
AuthorsDai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of hemagglutinin from influenza virus A/Sichuan/2/1987 (H3N2)
Authors: Dai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_validate_close_contact / 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 / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _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_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 / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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)343,73936
Polymers334,9116
Non-polymers8,82830
Water14,448802
1
A: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,87018
Polymers167,4553
Non-polymers4,41415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19010 Å2
ΔGint30 kcal/mol
Surface area59990 Å2
MethodPISA
2
B: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,87018
Polymers167,4553
Non-polymers4,41415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19060 Å2
ΔGint32 kcal/mol
Surface area59860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.940, 149.940, 150.090
Angle α, β, γ (deg.)90.000, 135.010, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 326 or resid 335...
21(chain B and (resid 8 through 81 or resid 83...
31(chain C and (resid 8 through 81 or resid 83...
41(chain D and (resid 8 through 81 or resid 83...
51(chain E and (resid 8 through 81 or resid 83...
61(chain F and (resid 8 through 81 or resid 83...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYS(chain A and (resid 8 through 326 or resid 335...AA8 - 3261 - 319
12ILEILELEULEU(chain A and (resid 8 through 326 or resid 335...AA335 - 381328 - 374
13ARGARGHISHIS(chain A and (resid 8 through 326 or resid 335...AA383 - 393376 - 386
14ILEILEARGARG(chain A and (resid 8 through 326 or resid 335...AA395 - 405388 - 398
15GLNGLNLEULEU(chain A and (resid 8 through 326 or resid 335...AA407 - 496400 - 489
16ASNASNNAGNAG(chain A and (resid 8 through 326 or resid 335...AA - P498 - 706491
21ASNASNASNASN(chain B and (resid 8 through 81 or resid 83...BB8 - 811 - 74
22LYSLYSLEULEU(chain B and (resid 8 through 81 or resid 83...BB83 - 38176 - 374
23ARGARGHISHIS(chain B and (resid 8 through 81 or resid 83...BB383 - 393376 - 386
24ILEILEARGARG(chain B and (resid 8 through 81 or resid 83...BB395 - 405388 - 398
25ASNASNILEILE(chain B and (resid 8 through 81 or resid 83...BB498 - 502491 - 495
26NAGNAGNAGNAG(chain B and (resid 8 through 81 or resid 83...BQ - T700 - 706
31ASNASNASNASN(chain C and (resid 8 through 81 or resid 83...CC8 - 811 - 74
32LYSLYSLYSLYS(chain C and (resid 8 through 81 or resid 83...CC83 - 32676 - 319
33ILEILELEULEU(chain C and (resid 8 through 81 or resid 83...CC335 - 381328 - 374
34ARGARGHISHIS(chain C and (resid 8 through 81 or resid 83...CC383 - 393376 - 386
35ILEILEARGARG(chain C and (resid 8 through 81 or resid 83...CC395 - 405388 - 398
36GLNGLNLEULEU(chain C and (resid 8 through 81 or resid 83...CC407 - 496400 - 489
37ASNASNILEILE(chain C and (resid 8 through 81 or resid 83...CC498 - 502491 - 495
38NAGNAGNAGNAG(chain C and (resid 8 through 81 or resid 83...CU - X700 - 706
41ASNASNASNASN(chain D and (resid 8 through 81 or resid 83...DD8 - 811 - 74
42LYSLYSLYSLYS(chain D and (resid 8 through 81 or resid 83...DD83 - 32676 - 319
43ILEILELEULEU(chain D and (resid 8 through 81 or resid 83...DD335 - 381328 - 374
44GLNGLNLEULEU(chain D and (resid 8 through 81 or resid 83...DD407 - 496400 - 489
45GLNGLNLEULEU(chain D and (resid 8 through 81 or resid 83...DD407 - 496400 - 489
46ASNASNILEILE(chain D and (resid 8 through 81 or resid 83...DD498 - 502491 - 495
47NAGNAGNAGNAG(chain D and (resid 8 through 81 or resid 83...DY - BA700 - 706
51ASNASNASNASN(chain E and (resid 8 through 81 or resid 83...EE8 - 811 - 74
52LYSLYSLYSLYS(chain E and (resid 8 through 81 or resid 83...EE83 - 32676 - 319
53ILEILEASNASN(chain E and (resid 8 through 81 or resid 83...EE335 - 81328 - 74
54ASNASNNAGNAG(chain E and (resid 8 through 81 or resid 83...EE - FA8 - 7061
55GLNGLNLEULEU(chain E and (resid 8 through 81 or resid 83...EE407 - 496400 - 489
56ASNASNILEILE(chain E and (resid 8 through 81 or resid 83...EE498 - 502491 - 495
57NAGNAGNAGNAG(chain E and (resid 8 through 81 or resid 83...ECA - FA700 - 706
61ASNASNASNASN(chain F and (resid 8 through 81 or resid 83...FF8 - 811 - 74
62LYSLYSLYSLYS(chain F and (resid 8 through 81 or resid 83...FF83 - 32676 - 319
63ILEILELEULEU(chain F and (resid 8 through 81 or resid 83...FF335 - 381328 - 374
64ARGARGHISHIS(chain F and (resid 8 through 81 or resid 83...FF383 - 393376 - 386
65ILEILEARGARG(chain F and (resid 8 through 81 or resid 83...FF395 - 405388 - 398
66GLNGLNLEULEU(chain F and (resid 8 through 81 or resid 83...FF407 - 496400 - 489
67ASNASNILEILE(chain F and (resid 8 through 81 or resid 83...FF498 - 502491 - 495
68NAGNAGNAGNAG(chain F and (resid 8 through 81 or resid 83...FGA - JA700 - 706

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Components

#1: Protein
Hemagglutinin /


Mass: 55818.484 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Sichuan/2/1987(H3N2))
Strain: A/Sichuan/2/1987(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H9XCU1
#2: 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.: 6 / Source method: isolated from a natural 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
#3: 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.: 24 / Source method: isolated from a natural 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Hepes pH 7.0, 30% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Sep 27, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.31→47.47 Å / Num. obs: 143375 / % possible obs: 98.96 % / Redundancy: 2 % / CC1/2: 0.99 / Rpim(I) all: 0.08485 / Rrim(I) all: 0.12 / Net I/σ(I): 8.65
Reflection shellResolution: 2.31→2.393 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 13250 / CC1/2: 0.637 / Rpim(I) all: 0.5943 / Rrim(I) all: 0.8405 / % possible all: 92.18

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Cootmodel building
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YP5

2yp5


Resolution: 2.31→47.47 Å / Cross valid method: THROUGHOUT / σ(F): 40.13 / Phase error: 39.31
RfactorNum. reflection% reflection
Rfree0.2511 7308 5.1 %
Rwork0.2208 --
obs0.2299 143375 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.93 Å2 / Biso mean: 40.7368 Å2 / Biso min: 2.02 Å2
Refinement stepCycle: final / Resolution: 2.31→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23149 0 570 802 24521
Biso mean--52.47 27.85 -
Num. residues----2931
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14537X-RAY DIFFRACTION7.906TORSIONAL
12B14537X-RAY DIFFRACTION7.906TORSIONAL
13C14537X-RAY DIFFRACTION7.906TORSIONAL
14D14537X-RAY DIFFRACTION7.906TORSIONAL
15E14537X-RAY DIFFRACTION7.906TORSIONAL
16F14537X-RAY DIFFRACTION7.906TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3103-2.35010.34383520.32515766611880
2.3501-2.39280.35453840.32726777716195
2.3928-2.43870.31313340.3116932726695
2.4387-2.48840.33933530.29496802715595
2.4884-2.54240.33634180.29646806722494
2.5424-2.60140.30774340.28696777721194
2.6014-2.66640.31894280.27726767719594
2.6664-2.73830.33283160.28226898721496
2.7383-2.81870.32383140.27226946726096
2.8187-2.90940.35073260.26666860718695
2.9094-3.01310.26773180.25016888720696
3.0131-3.13330.27883890.2426857724695
3.1333-3.27540.264450.2276770721594
3.2754-3.44730.24112810.23156935721696
3.4473-3.66210.26433700.24676865723595
3.6621-3.9430.25063150.24166731704692
3.943-4.33630.18983210.17516776709794
4.3363-4.9560.15913270.1446947727496
4.956-6.21470.22374110.18356898730994
6.2147-20.42060.22883270.18037012733996

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