[English] 日本語
Yorodumi
- PDB-7s6p: The crystal structure of human ISG15 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s6p
TitleThe crystal structure of human ISG15
ComponentsUbiquitin-like protein ISG15
KeywordsSIGNALING PROTEIN / ISG15 / ubiquitin / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ISG15-protein conjugation / positive regulation of protein oligomerization / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions ...ISG15-protein conjugation / positive regulation of protein oligomerization / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / modification-dependent protein catabolic process / ISG15 antiviral mechanism / response to virus / protein tag activity / integrin binding / positive regulation of type II interferon production / Interferon alpha/beta signaling / defense response to virus / defense response to bacterium / innate immune response / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOsipiuk, J. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Wydorski, P. / Joachimiak, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nat Commun / Year: 2023
Title: Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.
Authors: Wydorski, P.M. / Osipiuk, J. / Lanham, B.T. / Tesar, C. / Endres, M. / Engle, E. / Jedrzejczak, R. / Mullapudi, V. / Michalska, K. / Fidelis, K. / Fushman, D. / Joachimiak, A. / Joachimiak, L.A.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-like protein ISG15
B: Ubiquitin-like protein ISG15
C: Ubiquitin-like protein ISG15
D: Ubiquitin-like protein ISG15
E: Ubiquitin-like protein ISG15
F: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)103,8296
Polymers103,8296
Non-polymers00
Water2,144119
1
A: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3051
Polymers17,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3051
Polymers17,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3051
Polymers17,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3051
Polymers17,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3051
Polymers17,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3051
Polymers17,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.210, 134.862, 78.016
Angle α, β, γ (deg.)90.000, 108.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA3 - 1525 - 154
21LEULEUBB3 - 1525 - 154
12ARGARGAA3 - 1535 - 155
22ARGARGCC3 - 1535 - 155
13ASNASNAA3 - 1515 - 153
23ASNASNDD3 - 1515 - 153
14ARGARGAA3 - 1535 - 155
24ARGARGEE3 - 1535 - 155
15ARGARGAA3 - 1535 - 155
25ARGARGFF3 - 1535 - 155
16LEULEUBB3 - 1525 - 154
26LEULEUCC3 - 1525 - 154
17ASNASNBB3 - 1515 - 153
27ASNASNDD3 - 1515 - 153
18LEULEUBB3 - 1525 - 154
28LEULEUEE3 - 1525 - 154
19ARGARGBB3 - 1535 - 155
29ARGARGFF3 - 1535 - 155
110ASNASNCC3 - 1515 - 153
210ASNASNDD3 - 1515 - 153
111ARGARGCC3 - 1535 - 155
211ARGARGEE3 - 1535 - 155
112ARGARGCC3 - 1535 - 155
212ARGARGFF3 - 1535 - 155
113ASNASNDD3 - 1515 - 153
213ASNASNEE3 - 1515 - 153
114LEULEUDD3 - 1525 - 154
214LEULEUFF3 - 1525 - 154
115ARGARGEE3 - 1535 - 155
215ARGARGFF3 - 1535 - 155

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein / hUCRP


Mass: 17304.764 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05161
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.04 M potassium phosphate, 16% PEG8000, 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→46.54 Å / Num. obs: 54460 / % possible obs: 98.3 % / Redundancy: 3.4 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Χ2: 1.274 / Net I/av σ(I): 21.2 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.15-2.192.80.9461.1225450.5110.8220.641.1470.91291.6
2.19-2.2330.87126830.5670.5771.0490.91197.1
2.23-2.273.10.74227250.6890.4880.8920.92598.1
2.27-2.323.30.6726870.7660.4280.7980.91598.5
2.32-2.373.30.57827730.8160.3680.6880.96798.4
2.37-2.423.20.45526150.8420.30.5480.9796.7
2.42-2.483.50.42427630.8840.2660.5020.95899.4
2.48-2.553.50.34427310.9260.2130.406199.7
2.55-2.623.50.26327610.9470.1640.3111.08899.6
2.62-2.713.50.23227420.9560.1460.2741.13699.1
2.71-2.813.50.17927270.970.1130.2121.16298.7
2.81-2.923.30.14327040.9750.0930.1721.29798
2.92-3.053.30.11127260.9860.0710.1331.44698.3
3.05-3.213.60.09427660.9880.0580.1111.60799.7
3.21-3.413.50.07927380.9920.0490.0931.71199.5
3.41-3.683.50.06727440.9920.0420.081.83398.8
3.68-4.053.30.05427000.9940.0340.0641.5997.5
4.05-4.633.60.04827940.9960.030.0571.70799.9
4.63-5.833.40.04527260.9950.0290.0531.65698
5.83-46.543.50.04228100.9970.0270.051.36398.9

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z2M

1z2m


Resolution: 2.15→46.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 21.209 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 2625 4.8 %RANDOM
Rwork0.2205 ---
obs0.2228 51806 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.57 Å2 / Biso mean: 54.089 Å2 / Biso min: 30.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0 Å2-3.23 Å2
2---0.05 Å20 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 2.15→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6965 0 0 119 7084
Biso mean---44.77 -
Num. residues----903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137129
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177004
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.6319673
X-RAY DIFFRACTIONr_angle_other_deg1.2511.57716145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4645908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5723.483333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.268151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4431536
X-RAY DIFFRACTIONr_chiral_restr0.0650.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021540
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A42930.1
12B42930.1
21A43620.1
22C43620.1
31A42830.1
32D42830.1
41A43250.12
42E43250.12
51A42060.11
52F42060.11
61B43530.1
62C43530.1
71B42920.11
72D42920.11
81B42980.11
82E42980.11
91B42400.11
92F42400.11
101C42650.1
102D42650.1
111C43460.1
112E43460.1
121C42440.1
122F42440.1
131D42900.11
132E42900.11
141D41700.12
142F41700.12
151E42220.11
152F42220.11
LS refinement shellResolution: 2.152→2.207 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 188 -
Rwork0.412 3546 -
all-3734 -
obs--91.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.33910.07671.14861.13940.76294.155-0.13640.03050.0438-0.07640.014-0.0544-0.37160.05680.12250.3188-0.14060.01810.07840.01340.075531.875267.427652.7934
20.66370.11051.35121.3183-0.50413.1759-0.2575-0.01960.111-0.17540.06360.0846-0.4333-0.03690.19380.3330.0446-0.00860.10470.00210.07989.335467.339860.0249
30.85410.89551.3772.20911.70192.2823-0.0026-0.0451-0.02090.2771-0.0003-0.0260.0193-0.06160.00290.4035-0.06080.0060.0183-0.00470.104717.444734.979177.6323
40.0650.36560.08315.0590.40270.11350.1151-0.02040.00910.2999-0.1628-0.41280.1364-0.03550.04770.2754-0.0277-0.02460.05050.01140.245638.166732.823367.1807
50.1691-0.78940.21253.808-0.76020.92580.07010.0037-0.0362-0.2813-0.00010.25820.22030.0108-0.070.22430.0285-0.08420.04330.00120.27162.26634.131643.2777
60.7441-0.85211.413.6604-1.74152.6944-0.05570.06340.0281-0.3646-0.01670.1577-0.05610.15210.07230.2750.08490.01510.0980.03940.073823.453436.076933.3508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 153
2X-RAY DIFFRACTION2B2 - 153
3X-RAY DIFFRACTION3C3 - 153
4X-RAY DIFFRACTION4D3 - 152
5X-RAY DIFFRACTION5E3 - 153
6X-RAY DIFFRACTION6F3 - 153

+
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