[English] 日本語
Yorodumi
- PDB-3rzw: Crystal Structure of the Monobody ySMB-9 bound to human SUMO1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rzw
TitleCrystal Structure of the Monobody ySMB-9 bound to human SUMO1
Components
  • Monobody ySMB-9
  • Small ubiquitin-related modifier 1
KeywordsPROTEIN BINDING / Beta Sandwich / Beta Grasp / Antibody mimic / Engineered Binding Protein / Post-translational Modification
Function / homology
Function and homology information


protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / septin ring / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-like protein ligase binding / negative regulation of DNA binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein tag activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / nuclear body / protein stabilization / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Immunoglobulins ...Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGilbreth, R.N. / Koide, S.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold.
Authors: Koide, A. / Wojcik, J. / Gilbreth, R.N. / Hoey, R.J. / Koide, S.
History
DepositionMay 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monobody ySMB-9
B: Monobody ySMB-9
C: Small ubiquitin-related modifier 1
D: Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3186
Polymers43,1344
Non-polymers1842
Water2,486138
1
A: Monobody ySMB-9
D: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)21,5672
Polymers21,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-7 kcal/mol
Surface area9100 Å2
MethodPISA
2
B: Monobody ySMB-9
C: Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7514
Polymers21,5672
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.347, 97.829, 96.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Monobody ySMB-9


Mass: 10305.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 11261.608 Da / Num. of mol.: 2 / Mutation: C52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63165
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: 24% PEG-8000, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 23917 / Num. obs: 23917 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.15→2.19 Å / % possible all: 96.6

-
Processing

Software
NameVersionClassification
MAR345data collection
MD2data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.078 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23746 1217 5.1 %RANDOM
Rwork0.18636 ---
obs0.18895 22699 98.21 %-
all-22699 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.792 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2---0.14 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 12 138 2804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222736
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9573719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6425329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30224.355124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52615446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0351510
X-RAY DIFFRACTIONr_chiral_restr0.1370.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212084
X-RAY DIFFRACTIONr_mcbond_it0.9061.51647
X-RAY DIFFRACTIONr_mcangle_it1.66222681
X-RAY DIFFRACTIONr_scbond_it2.55631089
X-RAY DIFFRACTIONr_scangle_it4.0134.51037
LS refinement shellResolution: 2.152→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 90 -
Rwork0.231 1616 -
obs--96.11 %
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)
14.46120.4425-2.69430.7994-0.27653.02610.0395-0.1701-0.0020.0447-0.0240.0075-0.00920.1546-0.01540.0352-0.0113-0.01940.05330.03970.041854.26720.2243.021
21.2566-1.15070.92486.0394-3.04322.5759-0.073600.03270.17810.0319-0.039-0.1114-0.01760.04160.03690.0132-0.00720.0347-0.03560.04219.0022.592-25.626
33.02210.655-0.27483.51380.68024.0665-0.0045-0.00880.00610.01180.0198-0.0327-0.0414-0.0912-0.01540.0550.0088-0.03820.0239-0.00250.027533.592-18.681-13.895
43.7968-1.55050.49633.40140.05341.42690.04550.04960.07530.01510.006-0.0147-0.00070.0147-0.05140.0281-0.012-0.0060.09330.02370.010933.73629.63-14.643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 90
2X-RAY DIFFRACTION2B2 - 90
3X-RAY DIFFRACTION3C20 - 94
4X-RAY DIFFRACTION4D20 - 97

+
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