1F45

HUMAN INTERLEUKIN-12

> Summary

Summary for 1F45

Related1F42
DescriptorINTERLEUKIN-12 BETA CHAIN COMPLEX WITH INTERLEUKIN-12 ALPHA CHAIN
Functional Keywordsinterleukin, cytokine, cytokine-cytokine complex, cytokine/cytokine
Biological sourceHomo sapiens (human)
Total number of polymer chains3
Total molecular weight57895.02
Authors
Yoon, C.,Johnston, S.C.,Tang, J.,Tobin, J.F.,Somers, W.S. (deposition date: 2000-06-07, release date: 2001-06-20, modification date: 2011-07-13)
Primary citation
Yoon, C.,Johnston, S.C.,Tang, J.,Stahl, M.,Tobin, J.F.,Somers, W.S.
Charged residues dominate a unique interlocking topography in the heterodimeric cytokine interleukin-12.
EMBO J., 19:3530-3541, 2000
PubMed: 10899108
DOI: 10.1093/emboj/19.14.3530
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.8 Å)
?

Structure validation

ClashscoreRamachandran outliersSidechain outliers335.8%13.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1f45
no rotation
Molmil generated image of 1f45
rotated about x axis by 90°
Molmil generated image of 1f45
rotated about y axis by 90°

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight57895.0
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight57895.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.8 Å)

Cell axes112.900154.200101.700
Cell angles90.0090.0090.00
SpacegroupC 2 2 21
Resolution limits12.00 - 2.80
the highest resolution shell value -
R-factor0.241
R-work0.24100
R-free0.28400
RMSD bond length0.019
RMSD bond angle2.200

Data Collection Statistics

Resolution limits12.00 - 2.80
the highest resolution shell value2.90* - 2.80*
Number of reflections21109
Rmerge_l_obs0.066
the highest resolution shell value0.348
Completeness96.0
the highest resolution shell value96.*
Redundancy5.4
the highest resolution shell value3.2
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP5298 (18*)*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein10 (mg/ml)
21dropTris10 (mM)
31drop100 (mM)
41reservoirMPD12 (%(v/v))
51reservoir550 (mM)
61reservoirsodium acetate100 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
B0005737cellular_componentcytoplasm
B0005576cellular_componentextracellular region
B0005615cellular_componentextracellular space
B0043514cellular_componentinterleukin-12 complex
B0042163molecular_functioninterleukin-12 beta subunit binding
B0005143molecular_functioninterleukin-12 receptor binding
B0045513molecular_functioninterleukin-27 binding
B0046982molecular_functionprotein heterodimerization activity
B0007050biological_processcell cycle arrest
B0016477biological_processcell migration
B0071222biological_processcellular response to lipopolysaccharide
B0098586biological_processcellular response to virus
B0050830biological_processdefense response to Gram-positive bacterium
B0042832biological_processdefense response to protozoan
B0097191biological_processextrinsic apoptotic signaling pathway
B0006955biological_processimmune response
B0032700biological_processnegative regulation of interleukin-17 production
B0048662biological_processnegative regulation of smooth muscle cell proliferation
B0045785biological_processpositive regulation of cell adhesion
B2000510biological_processpositive regulation of dendritic cell chemotaxis
B0032729biological_processpositive regulation of interferon-gamma production
B0050671biological_processpositive regulation of lymphocyte proliferation
B0032946biological_processpositive regulation of mononuclear cell proliferation
B0032816biological_processpositive regulation of natural killer cell activation
B0045954biological_processpositive regulation of natural killer cell mediated cytotoxicity
B0002860biological_processpositive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
B0051135biological_processpositive regulation of NK T cell activation
B0034393biological_processpositive regulation of smooth muscle cell apoptotic process
B0045582biological_processpositive regulation of T cell differentiation
B0001916biological_processpositive regulation of T cell mediated cytotoxicity
B0042102biological_processpositive regulation of T cell proliferation
B0042520biological_processpositive regulation of tyrosine phosphorylation of Stat4 protein
B0032496biological_processresponse to lipopolysaccharide
B0010224biological_processresponse to UV-B
B0009615biological_processresponse to virus
A0005737cellular_componentcytoplasm
A0005576cellular_componentextracellular region
A0005615cellular_componentextracellular space
A0043514cellular_componentinterleukin-12 complex
A0070743cellular_componentinterleukin-23 complex
A0016020cellular_componentmembrane
A0004896molecular_functioncytokine receptor activity
A0042802molecular_functionidentical protein binding
A0042164molecular_functioninterleukin-12 alpha subunit binding
A0005143molecular_functioninterleukin-12 receptor binding
A0046982molecular_functionprotein heterodimerization activity
A0007050biological_processcell cycle arrest
A0016477biological_processcell migration
A0071346biological_processcellular response to interferon-gamma
A0071222biological_processcellular response to lipopolysaccharide
A0050829biological_processdefense response to Gram-negative bacterium
A0042832biological_processdefense response to protozoan
A0051607biological_processdefense response to virus
A0042095biological_processinterferon-gamma biosynthetic process
A0030101biological_processnatural killer cell activation
A0002323biological_processnatural killer cell activation involved in immune response
A0044130biological_processnegative regulation of growth of symbiont in host
A0002862biological_processnegative regulation of inflammatory response to antigenic stimulus
A0032693biological_processnegative regulation of interleukin-10 production
A0032700biological_processnegative regulation of interleukin-17 production
A0048662biological_processnegative regulation of smooth muscle cell proliferation
A0042104biological_processpositive regulation of activated T cell proliferation
A0010535biological_processpositive regulation of activation of JAK2 kinase activity
A0045785biological_processpositive regulation of cell adhesion
A0002230biological_processpositive regulation of defense response to virus by host
A0032725biological_processpositive regulation of granulocyte macrophage colony-stimulating factor production
A0050729biological_processpositive regulation of inflammatory response
A0045078biological_processpositive regulation of interferon-gamma biosynthetic process
A0032729biological_processpositive regulation of interferon-gamma production
A0032733biological_processpositive regulation of interleukin-10 production
A0032735biological_processpositive regulation of interleukin-12 production
A0032740biological_processpositive regulation of interleukin-17 production
A0050671biological_processpositive regulation of lymphocyte proliferation
A0043382biological_processpositive regulation of memory T cell differentiation
A0032946biological_processpositive regulation of mononuclear cell proliferation
A0032816biological_processpositive regulation of natural killer cell activation
A0002860biological_processpositive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
A0032819biological_processpositive regulation of natural killer cell proliferation
A0042346biological_processpositive regulation of NF-kappaB import into nucleus
A0051135biological_processpositive regulation of NK T cell activation
A0051142biological_processpositive regulation of NK T cell proliferation
A0045672biological_processpositive regulation of osteoclast differentiation
A0034393biological_processpositive regulation of smooth muscle cell apoptotic process
A0001916biological_processpositive regulation of T cell mediated cytotoxicity
A0042102biological_processpositive regulation of T cell proliferation
A0002827biological_processpositive regulation of T-helper 1 type immune response
A2000330biological_processpositive regulation of T-helper 17 cell lineage commitment
A2000318biological_processpositive regulation of T-helper 17 type immune response
A0034105biological_processpositive regulation of tissue remodeling
A0032760biological_processpositive regulation of tumor necrosis factor production
A0042517biological_processpositive regulation of tyrosine phosphorylation of Stat3 protein
A0042520biological_processpositive regulation of tyrosine phosphorylation of Stat4 protein
A0042523biological_processpositive regulation of tyrosine phosphorylation of Stat5 protein
A0042035biological_processregulation of cytokine biosynthetic process
A0042510biological_processregulation of tyrosine phosphorylation of Stat1 protein
A0010224biological_processresponse to UV-B
A0019233biological_processsensory perception of pain
A0019953biological_processsexual reproduction
A0042088biological_processT-helper 1 type immune response
A0042093biological_processT-helper cell differentiation
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE NAG A 501
ChainResidue
ATRP2
AGLU12
AHIS83
AASP191
AASN200
ANAG

AC24BINDING SITE FOR RESIDUE NAG A 502
ChainResidue
ATRP2
AGLU12
ANAG
AMAN

AC31BINDING SITE FOR RESIDUE MAN A 503
ChainResidue
ANAG

?

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
NAG_1f45_A_5023N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AILE1-TRP2NAG: N-ACETYL-D-GLUCOSAMINE
AGLU12NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1f45_A_5018N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ATRP2NAG: N-ACETYL-D-GLUCOSAMINE
AVAL10NAG: N-ACETYL-D-GLUCOSAMINE
AGLU12NAG: N-ACETYL-D-GLUCOSAMINE
AHIS83NAG: N-ACETYL-D-GLUCOSAMINE
ATRP90NAG: N-ACETYL-D-GLUCOSAMINE
AASP191NAG: N-ACETYL-D-GLUCOSAMINE
ATYR198NAG: N-ACETYL-D-GLUCOSAMINE
AASN200NAG: N-ACETYL-D-GLUCOSAMINE

?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
?

Catalytic Information from CSA

site_idNumber of ResiduesDetails
?

Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan