[English] 日本語
Yorodumi
- PDB-1rd8: Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rd8
TitleCrystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)
Components(hemagglutinin) x 2
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / MEMBRANE-FUSION PRECURSOR / VIRUS/VIRAL PROTEIN
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
PHOSPHATE ION / : / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStevens, J. / Corper, A.L. / Basler, C.F. / Taubenberger, J.K. / Palese, P. / Wilson, I.A.
CitationJournal: Science / Year: 2004
Title: Structure of the Uncleaved Human H1 Hemagglutinin from the Extinct 1918 Influenza Virus.
Authors: Stevens, J. / Corper, A.L. / Basler, C.F. / Taubenberger, J.K. / Palese, P. / Wilson, I.A.
History
DepositionNov 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hemagglutinin
B: hemagglutinin
C: hemagglutinin
D: hemagglutinin
E: hemagglutinin
F: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,67016
Polymers173,3266
Non-polymers3,34410
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38050 Å2
ΔGint-99 kcal/mol
Surface area58520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.529, 109.953, 136.238
Angle α, β, γ (deg.)90.00, 108.63, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 0

Dom-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUARGAA10 - 3298 - 335
2GLYGLYBB1 - 1751 - 175
3GLUARGCC10 - 3298 - 335
4GLYGLYDD1 - 1751 - 175
5GLUARGEE10 - 3298 - 335
6GLYGLYFF1 - 1751 - 175

-
Components

-
Protein , 2 types, 6 molecules ACEBDF

#1: Protein hemagglutinin /


Mass: 36971.398 Da / Num. of mol.: 3 / Fragment: Receptor binding domain, HA1 (residues 11-329)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Gene: Hemagglutinin / Plasmid: pAcGP67A / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 4325039, UniProt: Q9WFX3*PLUS
#2: Protein hemagglutinin /


Mass: 20803.992 Da / Num. of mol.: 3 / Fragment: Membrane fusion domain, HA2 (residues 1-175)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Gene: Hemagglutinin / Plasmid: pAcGP67A / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 4325039, UniProt: Q9WFX3*PLUS

-
Sugars , 3 types, 9 molecules

#3: 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
#4: 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.: 1
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
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

-
Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: sodium phosphate, potassium phosphate, sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
21.68 Msodium dihydrogen phosphate1reservoir
30.32 Mdipotassium hydrogen phosphate1reservoir
40.1 Mphosphate citrate1reservoirpH5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 51346 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.146 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.07 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 3368 / Rsym value: 0.52 / % possible all: 86
Reflection
*PLUS
Lowest resolution: 49.4 Å / Num. measured all: 125868 / Rmerge(I) obs: 0.146
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 95.1 % / Num. unique obs: 3368 / Rmerge(I) obs: 0.52

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.39 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.824 / SU B: 17.83 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 2.586 / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The chains were renumbered to be consistent with numbering of the biologically active molecule for which there are existing pdb entries for similar proteins. Renumbering changes made were: ...Details: The chains were renumbered to be consistent with numbering of the biologically active molecule for which there are existing pdb entries for similar proteins. Renumbering changes made were: Segment A 1-503 was split to Chains A 10-329 and Chain B 1-175; Segment B 1-503 was split to Chains C 10-329 and Chain D 1-175; Segment C 1-503 was split to Chains E 10-329 and Chain F 1-175.
RfactorNum. reflection% reflectionSelection details
Rfree0.29522 2573 5 %RANDOM
Rwork0.26998 ---
all0.302 51345 --
obs0.27128 48772 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.312 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.42 Å2
2---0.22 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 3→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11865 0 217 0 12082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02112190
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210336
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.95516573
X-RAY DIFFRACTIONr_angle_other_deg1.032324059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60951505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.21802
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213669
X-RAY DIFFRACTIONr_gen_planes_other0.010.022421
X-RAY DIFFRACTIONr_nbd_refined0.240.23057
X-RAY DIFFRACTIONr_nbd_other0.2530.213064
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.27201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.4681.57447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.765211943
X-RAY DIFFRACTIONr_scbond_it3.35334743
X-RAY DIFFRACTIONr_scangle_it5.1784.54630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2549tight positional0.040.05
3C2549tight positional0.040.05
5E2549tight positional0.030.05
2B1406tight positional0.040.05
4D1406tight positional0.040.05
6F1406tight positional0.030.05
1A2549tight thermal0.080.5
3C2549tight thermal0.080.5
5E2549tight thermal0.080.5
2B1406tight thermal0.080.5
4D1406tight thermal0.080.5
6F1406tight thermal0.080.5
LS refinement shellResolution: 3→3.079 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.416 169
Rwork0.458 3397
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 49.4 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.85

+
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