OCA Atlas for 1RD8

1RD8

Viral Protein

date

Nov 05, 2003

title

Crystal Structure Of The 1918 Human H1 Hemagglutinin Precurs

authors

J.Stevens, A.L.Corper, C.F.Basler, J.K.Taubenberger, P.Palese, I.

compound

source

Molecule: Hemagglutinin
Chain: A, C, E
Fragment: Receptor Binding Domain, Ha1 (Residues 11-329)
Engineered: Yes

Organism_scientific: Influenza A Virus
Organism_taxid: 11320
Gene: Hemagglutinin
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pacgp67a

Molecule: Hemagglutinin
Chain: B, D, F
Fragment: Membrane Fusion Domain, Ha2 (Residues 1-175)
Engineered: Yes

symmetry

Space Group: C 1 2 1

R_factor

0.270

R_Free

0.295

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
190.529	109.953	136.238	90.00	108.63	90.00

method

X-Ray Diffraction

resolution

3.00 Å

ligand

BMA, MAN, NAG, PO4

enzyme

note

1RD8 (Molecule of the Month:pdb76)

related structures

by homologous chain: 1RUZ

Gene
Ontology

Chain	Function	Process	Component
A, C, E
F, D, B

Primary reference

Structure of the uncleaved human h1 hemagglutinin from the extinct 1918 influenza virus., Stevens J, Corper AL, Basler CF, Taubenberger JK, Palese P, Wilson IA, Science 2004 Mar 19;303(5665):1866-70. Epub 2004 Feb 5. PMID:14764887

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk]

Biological Unit Coordinates (1rd8.pdb1.gz) 240 Kb

LPC: Ligand-Protein Contacts for 1RD8

CSU: Contacts of Structural Units for 1RD8

Likely Quarternary Molecular Structure file(s) for 1RD8

Structure Factors (327 Kb)

Retrieve 1RD8 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1RD8 from S2C, [Save to disk]

Re-refined 1rd8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RD8 in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1RD8

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1RD8, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1rd8a_, region A [Jmol] [rasmolscript] [script source]
- Domain d1rd8b_, region B [Jmol] [rasmolscript] [script source]
- Domain d1rd8c_, region C [Jmol] [rasmolscript] [script source]
- Domain d1rd8d_, region D [Jmol] [rasmolscript] [script source]
- Domain d1rd8e_, region E [Jmol] [rasmolscript] [script source]
- Domain d1rd8f_, region F [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1rd8_E] [1rd8_A] [1rd8] [1rd8_C] [1rd8_D] [1rd8_B] [1rd8_F]

SWISS-PROT database: [Q9WFX3]

Domain organization of [HEMA_I18A0] by SWISSPFAM

Other resources with information on 1RD8

Community annotation for 1RD8 at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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