[English] 日本語
Yorodumi
- PDB-1rh2: RECOMBINANT HUMAN INTERFERON-ALPHA 2B -

+
Open data


ID or keywords:

Loading...

-
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 / B cell activation involved in immune response / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / host-mediated suppression of symbiont invasion / cell surface receptor signaling pathway via STAT ...type I interferon receptor binding / B cell activation involved in immune response / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / host-mediated suppression of symbiont invasion / cell surface receptor signaling pathway via STAT / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / response to exogenous dsRNA / humoral immune response / Regulation of IFNA/IFNB signaling / cytokine activity / Evasion by RSV of host interferon responses / cellular response to virus / Interferon alpha/beta signaling / cell-cell signaling / : / Factors involved in megakaryocyte development and platelet production / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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.

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more