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- PDB-1rh2: RECOMBINANT HUMAN INTERFERON-ALPHA 2B -

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Basic information

Entry
Database: PDB / ID: 1rh2
TitleRECOMBINANT HUMAN INTERFERON-ALPHA 2B
ComponentsINTERFERON-ALPHA 2B
KeywordsCYTOKINE / INTERFERON / ANTI-VIRAL / IMMUNOMODULATOR / 4 HELIX BUNDLE
Function / homology
Function and homology information


type I interferon receptor binding / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell ...type I interferon receptor binding / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / response to exogenous dsRNA / B cell proliferation / humoral immune response / Regulation of IFNA/IFNB signaling / B cell differentiation / cytokine activity / Evasion by RSV of host interferon responses / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / collagen-containing extracellular matrix / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.9 Å
AuthorsWalter, M.R.
CitationJournal: Structure / Year: 1996
Title: Zinc mediated dimer of human interferon-alpha 2b revealed by X-ray crystallography.
Authors: Radhakrishnan, R. / Walter, L.J. / Hruza, A. / Reichert, P. / Trotta, P.P. / Nagabhushan, T.L. / Walter, M.R.
History
DepositionNov 7, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERFERON-ALPHA 2B
B: INTERFERON-ALPHA 2B
C: INTERFERON-ALPHA 2B
D: INTERFERON-ALPHA 2B
E: INTERFERON-ALPHA 2B
F: INTERFERON-ALPHA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,92410
Polymers115,6626
Non-polymers2624
Water00
1
A: INTERFERON-ALPHA 2B
hetero molecules


  • defined by author
  • 19.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)19,3422
Polymers19,2771
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: INTERFERON-ALPHA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3422
Polymers19,2771
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: INTERFERON-ALPHA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3422
Polymers19,2771
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: INTERFERON-ALPHA 2B


Theoretical massNumber of molelcules
Total (without water)19,2771
Polymers19,2771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: INTERFERON-ALPHA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3422
Polymers19,2771
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: INTERFERON-ALPHA 2B


Theoretical massNumber of molelcules
Total (without water)19,2771
Polymers19,2771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.400, 75.500, 148.200
Angle α, β, γ (deg.)90.00, 90.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.998, -0.045, -0.036), (0.042, -0.128, -0.991), (0.04, -0.991, 0.129)86.804, 124.765, 109.34
2given(-0.984, -0.105, -0.142), (0.058, -0.952, 0.302), (-0.167, 0.289, 0.943)120.795, 60.644, -39.301
3given(0.997, 0.067, 0.025), (-0.017, -0.126, 0.992), (0.07, -0.99, -0.125)19.05, -25.903, 90.211
4given(0.991, 0.119, 0.055), (-0.119, 0.993, 0.002), (-0.055, -0.009, 0.998)-7.078, -5.137, -72.188
5given(-0.971, -0.114, -0.209), (0.224, -0.142, -0.964), (0.08, -0.983, 0.164)104.108, 105.491, 29.863

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Components

#1: Protein
INTERFERON-ALPHA 2B / Coordinate model: Cα atoms only


Mass: 19277.033 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01563
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Compound detailsTHE DISULFIDE BOND BETWEEN CYS 1 AND CYS 98 IS NOT OBSERVED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growMethod: macroseeding / pH: 5.6
Details: PROTEIN WAS CRYSTALLIZED FROM 40MM ZINC ACETATE, 30MM CACODYLATE, PH 5.6; MACRO SEEDING WAS PERFORMED TO GET REASONABLE SIZE CRYSTALS., macroseeding
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
240 mM1reservoirZnAc2
330 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1995
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→6 Å / Num. obs: 31925 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.2 / % possible all: 92
Reflection
*PLUS
Num. measured all: 217393

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Processing

Software
NameVersionClassification
MOLECULARSTRUCTURE CORP.data collection
MOLECULARSTRUCTURE CORP.data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MSCdata reduction
MSCdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.9→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.1
Details: SIX MOLECULES IN THE ASYMMETRIC UNIT WERE REFINED WITH NCS RESTRAINTS WITH WEIGHT = 30 KCAL/MOL-(A)2 AND SIGB = 1.5 (A)2
RfactorNum. reflection% reflectionSelection details
Rfree0.311 1326 4.9 %RANDOM
Rwork0.227 ---
obs0.227 27010 99.2 %-
Displacement parametersBiso mean: 30.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.34 Å
Luzzati d res low-6 Å
Luzzati sigma a0.49 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 4 0 791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.58
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.9→3.02 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.393 -4.3 %
Rwork0.319 3083 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2ZINC.PARZINC.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58

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