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- PDB-1au1: HUMAN INTERFERON-BETA CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1au1
TitleHUMAN INTERFERON-BETA CRYSTAL STRUCTURE
ComponentsINTERFERON-BETA
KeywordsINTERFERON / HELICAL CYTOKINE / IMMUNE SYSTEM / CYTOKINE
Function / homology
Function and homology information


regulation of MHC class I biosynthetic process / B cell activation involved in immune response / type I interferon receptor binding / chloramphenicol O-acetyltransferase activity / 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 / natural killer cell activation ...regulation of MHC class I biosynthetic process / B cell activation involved in immune response / type I interferon receptor binding / chloramphenicol O-acetyltransferase activity / 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 / natural killer cell activation / positive regulation of innate immune response / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / response to exogenous dsRNA / cellular response to exogenous dsRNA / type I interferon-mediated signaling pathway / B cell proliferation / humoral immune response / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / positive regulation of apoptotic signaling pathway / B cell differentiation / cytokine activity / response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / blood coagulation / TRAF3-dependent IRF activation pathway / Factors involved in megakaryocyte development and platelet production / defense response to virus / Oxidative Stress Induced Senescence / adaptive immune response / cell surface receptor signaling pathway / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interferon beta / Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarpusas, M. / Nolte, M. / Lipscomb, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The crystal structure of human interferon beta at 2.2-A resolution.
Authors: Karpusas, M. / Nolte, M. / Benton, C.B. / Meier, W. / Lipscomb, W.N. / Goelz, S.
History
DepositionSep 9, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 25, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Refinement description / Structure summary
Category: atom_site / database_PDB_caveat / software
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _software.name
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / 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.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERFERON-BETA
B: INTERFERON-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6375
Polymers40,1082
Non-polymers1,5293
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-22 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.300, 65.900, 121.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INTERFERON-BETA


Mass: 20054.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01574
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D-quinovopyranose-(1-6)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 1137.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-2DGlcpb1-3DGlcpb1-4DGlcpb1-4[DQuipa1-6]DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a2122m-1a_1-5]/1-1-1-1-1-1-2/a4-b1_a6-g1_b4-c1_c3-d1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}[(6+1)][a-D-6-deoxy-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-quinovopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuipa1-6DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-6-deoxy-Glcp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.83 Å3/Da / Density % sol: 55.43 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
225 mMsodium acetate1drop
314 %PEG40001reservoir
40.1 Msodium acetate1reservoir
50.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 10, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 18405 / % possible obs: 83.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0766

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Processing

Software
NameVersionClassification
bioteXdata collection
AMoREphasing
X-PLORmodel building
X-PLOR3.81refinement
bioteXdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES 28 - 30 OF MOLECULE B HAVE NOT BEEN MODELED DUE TO WEAK ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.283 -10 %RANDOM
Rwork0.223 ---
obs0.223 18405 83.1 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 113 243 3883
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.81 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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