[English] 日本語
Yorodumi
- PDB-3al4: Crystal structure of the swine-origin A (H1N1)-2009 influenza A v... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3al4
TitleCrystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN/VIRAL PROTEIN / TRIMER / ENVELOPE PROTEIN / HEMAGGLUTININ / VIRAL PROTEIN-VIRAL PROTEIN complex
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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: 2.872 Å
AuthorsZhang, W. / Qi, J.X. / Shi, Y. / Li, Q. / Yan, J.H. / Gao, G.F.
CitationJournal: Protein Cell / Year: 2010
Title: Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus
Authors: Zhang, W. / Qi, J. / Shi, Y. / Li, Q. / Gao, F. / Sun, Y. / Lu, X. / Lu, Q. / Vavricka, C.J. / Liu, D. / Yan, J. / Gao, G.F.
History
DepositionJul 22, 2010Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 4, 2010ID: 3LYJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: 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.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 / _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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.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 1, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)353,31535
Polymers346,48112
Non-polymers6,83423
Water5,711317
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0386
Polymers57,7472
Non-polymers1,2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-41 kcal/mol
Surface area23620 Å2
MethodPISA
2
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2006
Polymers57,7472
Non-polymers1,4534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-41 kcal/mol
Surface area23650 Å2
MethodPISA
3
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0567
Polymers57,7472
Non-polymers1,3095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-42 kcal/mol
Surface area23700 Å2
MethodPISA
4
G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4105
Polymers57,7472
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-39 kcal/mol
Surface area23530 Å2
MethodPISA
5
I: Hemagglutinin
J: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7584
Polymers57,7472
Non-polymers1,0112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-41 kcal/mol
Surface area23430 Å2
MethodPISA
6
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8537
Polymers57,7472
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-42 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.020, 115.190, 114.985
Angle α, β, γ (deg.)62.31, 77.94, 81.05
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin /


Mass: 36989.715 Da / Num. of mol.: 6 / Fragment: UNP residues 18-344
Source method: isolated from a genetically manipulated source
Details: HEMAGGLUTININ HA1 / Source: (gene. exp.) Influenza A virus / Strain: A/CALIFORNIA/04/2009(H1N1) / Gene: HEMAGGLUTININ / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: C3W5S1
#2: Protein
Hemagglutinin /


Mass: 20757.035 Da / Num. of mol.: 6 / Fragment: UNP residues 345-520
Source method: isolated from a genetically manipulated source
Details: HEMAGGLUTININ HA2 / Source: (gene. exp.) Influenza A virus / Strain: A/CALIFORNIA/04/2009(H1N1) / Gene: HEMAGGLUTININ / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: C3W5S1

-
Sugars , 3 types, 23 molecules

#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.: 5
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: 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.: 16
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

-
Non-polymers , 1 types, 317 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.59 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.872→50 Å / Num. obs: 64796 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Biso Wilson estimate: 56.27 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 12.9
Reflection shellResolution: 2.87→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.501 / % possible all: 90.7

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(PHENIX.REFINE: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RU7
Resolution: 2.872→24.19 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 0.07 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 3085 5.05 %
Rwork0.246 57982 -
obs0.247 61067 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.94 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso max: 330.34 Å2 / Biso mean: 81.17 Å2 / Biso min: 16.64 Å2
Baniso -1Baniso -2Baniso -3
1--5.51 Å22.924 Å2-2.521 Å2
2--0.618 Å217.083 Å2
3---4.893 Å2
Refinement stepCycle: LAST / Resolution: 2.872→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22867 0 442 317 23626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423966
X-RAY DIFFRACTIONf_angle_d0.97132453
X-RAY DIFFRACTIONf_dihedral_angle_d19.6068661
X-RAY DIFFRACTIONf_chiral_restr0.0663553
X-RAY DIFFRACTIONf_plane_restr0.0044140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8716-2.91640.3783850.32541567X-RAY DIFFRACTION57
2.9164-2.96410.36681160.31792233X-RAY DIFFRACTION77
2.9641-3.01510.35271270.31522338X-RAY DIFFRACTION80
3.0151-3.06990.32851050.3172389X-RAY DIFFRACTION84
3.0699-3.12880.33021230.29332541X-RAY DIFFRACTION86
3.1288-3.19250.32731470.29532503X-RAY DIFFRACTION88
3.1925-3.26180.31231370.29112574X-RAY DIFFRACTION90
3.2618-3.33750.31831320.2842652X-RAY DIFFRACTION91
3.3375-3.42070.30811230.28042670X-RAY DIFFRACTION92
3.4207-3.51290.30911340.27822697X-RAY DIFFRACTION93
3.5129-3.6160.30331390.25762745X-RAY DIFFRACTION96
3.616-3.73230.28771620.25682787X-RAY DIFFRACTION97
3.7323-3.86520.24881500.24842823X-RAY DIFFRACTION97
3.8652-4.01920.27721370.24522787X-RAY DIFFRACTION97
4.0192-4.20130.25461730.2342737X-RAY DIFFRACTION97
4.2013-4.42150.24941540.22472915X-RAY DIFFRACTION99
4.4215-4.69660.25431510.2052788X-RAY DIFFRACTION98
4.6966-5.05620.26181480.21962862X-RAY DIFFRACTION99
5.0562-5.55940.23041800.20892826X-RAY DIFFRACTION99
5.5594-6.35120.26471720.2392821X-RAY DIFFRACTION99
6.3512-7.95420.26021400.22982883X-RAY DIFFRACTION100
7.9542-24.1880.1941500.19962844X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -20.2272 Å / Origin y: -28.1217 Å / Origin z: -32.6646 Å
111213212223313233
T0.1288 Å20.0127 Å2-0.0565 Å2-0.1607 Å20.009 Å2--0.1165 Å2
L0.2871 °20.1286 °2-0.1928 °2-0.2431 °2-0.0709 °2--0.1527 °2
S0.0345 Å °-0.0095 Å °-0.012 Å °0.0208 Å °-0.0623 Å °-0.1407 Å °-0.0011 Å °-0.0542 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA7 - 370
2X-RAY DIFFRACTION1ALLB1 - 307
3X-RAY DIFFRACTION1ALLC7 - 371
4X-RAY DIFFRACTION1ALLD1 - 265
5X-RAY DIFFRACTION1ALLE7 - 364
6X-RAY DIFFRACTION1ALLF2 - 284
7X-RAY DIFFRACTION1ALLG7 - 378
8X-RAY DIFFRACTION1ALLH1 - 277
9X-RAY DIFFRACTION1ALLI7 - 371
10X-RAY DIFFRACTION1ALLJ1 - 319
11X-RAY DIFFRACTION1ALLK7 - 369
12X-RAY DIFFRACTION1ALLL2 - 279

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more