OCA Atlas for 3D87

3D87

Cytokine

date

May 22, 2008

title

Crystal Structure Of Interleukin-23

authors

B.M.Beyer, R.Ingram, L.Ramanathan, P.Reichert, H.Le, V.Madison

compound

source

Molecule: Interleukin-23 Subunit P19
Chain: A, C
Fragment: Subunit P19
Synonym: Interleukin-23 Subunit Alpha; Il-23 Subunit Alpha; Il-23p19;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il23a, Sgrf, Unq2498pro5798
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: Hi-Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Dual

Molecule: Interleukin-12 Subunit P40
Chain: B, D
Fragment: Subunit P40
Synonym: Il-12b; Il-12 Subunit P40; Cytotoxic Lymphocyte Maturation Factor 40 Kda Subunit; Clmf P40; Nk Cell Stimulatory Factor Chain 2; Nksf2;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il12b, Nksf2
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: Hi-Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Dual

symmetry

Space Group: C 2 2 21

R_factor

0.268

R_Free

0.323

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
110.098	240.587	141.781	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.90 Å

ligand

K, MAN, PO4

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, C	cytokine activity interleukin-23 receptor bind...	positive regulation of T cel... positive regulation of defen... positive regulation of T-hel... inflammatory response positive regulation of activ... negative regulation of inter... positive regulation of granu... positive regulation of inter... positive regulation of inter... positive regulation of inter... positive regulation of inter... positive regulation of tumor... positive regulation of natur... positive regulation of natur... positive regulation of tissu... T cell proliferation positive regulation of T cel... positive regulation of activ... positive regulation of NF-ka... regulation of tyrosine phosp... positive regulation of tyros... positive regulation of tyros... positive regulation of tyros... positive regulation of memor... innate immune response positive regulation of osteo... positive regulation of trans... tissue remodeling positive regulation of infla... defense response to Gram-neg... positive regulation of NK T ... positive regulation of NK T ... defense response to virus positive regulation of neutr... positive regulation of T-hel... positive regulation of T-hel...	extracellular region extracellular space interleukin-23 complex
D, B	cytokine activity cytokine receptor binding interleukin-12 receptor bind... protein binding growth factor activity interleukin-12 alpha subunit... identical protein binding protein homodimerization act... interleukin-23 receptor bind... protein heterodimerization a...	positive regulation of T cel... positive regulation of defen... positive regulation of T-hel... positive regulation of natur... negative regulation of infla... cell cycle arrest cell surface receptor signal... response to UV-B positive regulation of activ... cell migration cytokine-mediated signaling ... sexual reproduction natural killer cell activati... negative regulation of inter... negative regulation of inter... positive regulation of granu... positive regulation of inter... positive regulation of inter... positive regulation of inter... positive regulation of inter... positive regulation of tumor... positive regulation of natur... positive regulation of natur... positive regulation of tissu... positive regulation of smoot... regulation of cytokine biosy... T-helper 1 type immune respo... T-helper cell differentiatio... interferon-gamma biosyntheti... positive regulation of T cel... positive regulation of activ... positive regulation of NF-ka... regulation of tyrosine phosp... positive regulation of tyros... positive regulation of tyros... positive regulation of tyros... defense response to protozoa... positive regulation of memor... negative regulation of growt... positive regulation of inter... positive regulation of osteo... positive regulation of cell ... negative regulation of smoot... positive regulation of lymph... positive regulation of infla... defense response to Gram-neg... positive regulation of NK T ... positive regulation of NK T ... defense response to virus cellular response to lipopol... cellular response to interfe... positive regulation of T-hel... positive regulation of T-hel...	extracellular region extracellular space cytoplasm interleukin-12 complex interleukin-23 complex

Primary reference

Crystal Structures of the Pro-Inflammatory Cytokine Interleukin-23 and Its Complex with a High-Affinity Neutralizing Antibody., Beyer BM, Ingram R, Ramanathan L, Reichert P, Le HV, Madison V, Orth P, J Mol Biol. 2008 Aug 7. PMID:18708069

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]

Biological Unit Coordinates (3d87.pdb1.gz) 144 Kb

Biological Unit Coordinates (3d87.pdb2.gz) 74 Kb

Biological Unit Coordinates (3d87.pdb3.gz) 73 Kb

LPC: Ligand-Protein Contacts for 3D87

CSU: Contacts of Structural Units for 3D87

Likely Quarternary Molecular Structure file(s) for 3D87

Structure Factors (1222 Kb)

Retrieve 3D87 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3D87 from S2C, [Save to disk]

Re-refined 3d87 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3D87 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.

On AstexViewer, from MSD-EBI (viewer documentation).

On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3D87

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

3D motif for 3D87, from MSDmotif at EBI

Fold representative 3d87 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3d87_A] [3d87_B] [3d87_C] [3d87_D]

SWISS-PROT database: [P29460] [Q9NPF7]

Domain organization of [IL12B_HUMAN] [IL23A_HUMAN] by SWISSPFAM

Domains found in 3D87: [IGc2] [IL6 ] by SMART

Alignments of the sequence of 3D87 with the sequences similar proteins can be viewed for 3D87's classification [IL12B_HUMAN] [IL23A_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.

A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [IL12B_HUMAN] [IL23A_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3D87

Community annotation for 3D87 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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