[English] 日本語
Yorodumi
- PDB-9hin: Crystal structure of human TRIM7 PRYSPRY domain bound to ((S)-2-(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hin
TitleCrystal structure of human TRIM7 PRYSPRY domain bound to ((S)-2-(6-(6-methoxypyridin-3-yl)-1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine
ComponentsE3 ubiquitin-protein ligase TRIM7
KeywordsLIGASE / TRIM7 / PRYSPRY / E3 Ligase
Function / homology
Function and homology information


antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / innate immune response / Golgi apparatus / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
zinc finger of C3HC4-type, RING / Zinc finger, B-box, chordata / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...zinc finger of C3HC4-type, RING / Zinc finger, B-box, chordata / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / L(+)-TARTARIC ACID / E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLenz, C. / Haman, A. / Spissinger, H. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of human TRIM7 PRYSPRY domain bound to ((S)-2-(6-(6-methoxypyridin-3-yl)-1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine
Authors: Lenz, C. / Haman, A. / Spissinger, H. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionNov 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4754
Polymers19,7461
Non-polymers7293
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint3 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.784, 44.154, 57.343
Angle α, β, γ (deg.)90.00, 107.54, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein E3 ubiquitin-protein ligase TRIM7


Mass: 19746.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C029
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1IU9 / ((S)-2-(6-(6-methoxypyridin-3-yl)-1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine / (2~{S})-5-azanyl-2-[[(2~{S})-2-[5-(6-methoxypyridin-3-yl)-3-oxidanylidene-1~{H}-isoindol-2-yl]-3-phenyl-propanoyl]amino]-5-oxidanylidene-pentanoic acid


Type: peptide-like / Mass: 516.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1 M sodium tartrate, 100 mM citrate pH 5.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.55→54.68 Å / Num. obs: 31664 / % possible obs: 99.2 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 14.3
Reflection shellResolution: 1.55→1.58 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1543 / CC1/2: 0.903

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→54.68 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.082 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21873 1584 5 %RANDOM
Rwork0.18232 ---
obs0.18416 30033 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.593 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0.82 Å2
2---3.8 Å2-0 Å2
3---2.88 Å2
Refinement stepCycle: 1 / Resolution: 1.55→54.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 52 88 1467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121436
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161308
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6491955
X-RAY DIFFRACTIONr_angle_other_deg0.561.6082996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.25514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92710214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6981.84689
X-RAY DIFFRACTIONr_mcbond_other4.6531.839689
X-RAY DIFFRACTIONr_mcangle_it6.6093.306863
X-RAY DIFFRACTIONr_mcangle_other6.6093.308864
X-RAY DIFFRACTIONr_scbond_it5.0532.013747
X-RAY DIFFRACTIONr_scbond_other5.052.015748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1133.6251093
X-RAY DIFFRACTIONr_long_range_B_refined10.9318.151466
X-RAY DIFFRACTIONr_long_range_B_other10.86117.621458
X-RAY DIFFRACTIONr_rigid_bond_restr3.80832744
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 114 -
Rwork0.272 2182 -
obs--97.58 %
Refinement TLS params.Method: refined / Origin x: -15.68 Å / Origin y: -22.3999 Å / Origin z: 9.2611 Å
111213212223313233
T0.0613 Å20.0019 Å2-0.0446 Å2-0.0251 Å20.0083 Å2--0.0403 Å2
L3.5693 °2-0.8789 °20.5532 °2-2.6002 °2-0.1718 °2--2.9795 °2
S-0.2215 Å °-0.2425 Å °0.1169 Å °0.331 Å °0.0458 Å °-0.1711 Å °-0.1471 Å °0.0482 Å °0.1757 Å °

+
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