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- PDB-6trw: Crystal structure of DPP8 in complex with the EIL peptide (SLRFLF... -

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Basic information

Entry
Database: PDB / ID: 6trw
TitleCrystal structure of DPP8 in complex with the EIL peptide (SLRFLFEGQRIADNH)
Components
  • Dipeptidyl peptidase 8
  • SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
KeywordsHYDROLASE / EIL peptide / DPP8 / SUMO1
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) / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule ...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) / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / small protein activating enzyme binding / dipeptidyl-peptidase IV / 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 / dipeptidyl-peptidase activity / regulation of cardiac muscle cell contraction / SUMOylation of RNA binding proteins / negative regulation of programmed cell death / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / roof of mouth development / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / nuclear pore / aminopeptidase activity / Regulation of IFNG signaling / SUMOylation of DNA damage response and repair proteins / cellular response to cadmium ion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / negative regulation of DNA-binding transcription factor activity / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / nuclear membrane / protein stabilization / nuclear body / nuclear speck / immune response / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / apoptotic process / enzyme binding / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family ...Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Alpha/Beta hydrolase fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Small ubiquitin-related modifier 1 / Dipeptidyl peptidase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRoss, B. / Huber, R.
CitationJournal: J.Appl.Crystallogr. / Year: 2021
Title: Aerosol-based ligand soaking of reservoir-free protein crystals.
Authors: Ross, B. / Krapp, S. / Geiss-Friedlander, R. / Littmann, W. / Huber, R. / Kiefersauer, R.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 8
B: Dipeptidyl peptidase 8
C: Dipeptidyl peptidase 8
D: SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
E: SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
F: SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,1479
Polymers317,0786
Non-polymers693
Water59433
1
A: Dipeptidyl peptidase 8
D: SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
hetero molecules

A: Dipeptidyl peptidase 8
D: SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,4326
Polymers211,3864
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area8810 Å2
ΔGint-60 kcal/mol
Surface area65230 Å2
MethodPISA
2
B: Dipeptidyl peptidase 8
C: Dipeptidyl peptidase 8
E: SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
F: SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,4326
Polymers211,3864
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-58 kcal/mol
Surface area64550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.045, 245.283, 261.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dipeptidyl peptidase 8 / DP8 / Dipeptidyl peptidase IV-related protein 1 / DPRP-1 / Dipeptidyl peptidase VIII / DPP VIII / ...DP8 / Dipeptidyl peptidase IV-related protein 1 / DPRP-1 / Dipeptidyl peptidase VIII / DPP VIII / Prolyl dipeptidase DPP8


Mass: 103886.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP8, DPRP1, MSTP097, MSTP135, MSTP141 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6V1X1, dipeptidyl-peptidase IV
#2: Protein/peptide SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG


Mass: 1806.011 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P63165*PLUS
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.12 Å3/Da / Density % sol: 70.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75 / Details: 0.46 M Na citrate pH 6.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 3→49.17 Å / Num. obs: 104482 / % possible obs: 99.9 % / Redundancy: 8.427 % / Biso Wilson estimate: 77.091 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.097 / Χ2: 0.997 / Net I/σ(I): 20.41 / Num. measured all: 880465 / Scaling rejects: 90
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.088.5271.2711.9965281765876560.711.351100
3.08-3.168.37612.561787737973770.7941.065100
3.16-3.267.9150.673.5560462764376390.8790.71799.9
3.26-3.378.3390.4894.962859754375380.930.52199.9
3.37-3.498.8330.35766284750475040.970.371100
3.49-3.638.7710.2559.0664833739473920.9810.271100
3.63-3.88.6950.18612.0265978758875880.9890.197100
3.8-4.018.5750.13116.2463689742774270.9950.139100
4.01-4.268.0290.08721.9859883746174580.9970.093100
4.26-4.68.4920.06229.8963271745174510.9990.066100
4.6-5.078.7950.0536.5765300742574250.9990.053100
5.07-5.838.4970.0536.1162707738173800.9990.054100
5.83-7.17.9850.04637.6151645646864680.9990.049100
7.1-98.530.0355.3935006410541040.9990.032100
9-11.567.810.02171.23166362130213010.023100
11.56-16.877.5940.0279.1999181307130610.02299.9
16.87-278.0280.02184.71398249649610.022100
27-49.176.6010.02477.6994417614310.02681.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOO

6eoo


Resolution: 3→49.17 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 15.252 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.658 / ESU R Free: 0.316
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 5225 5 %RANDOM
Rwork0.1913 ---
obs0.193 99257 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 224.53 Å2 / Biso mean: 91.044 Å2 / Biso min: 48.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å2-0 Å2-0 Å2
2--4.85 Å20 Å2
3----2.78 Å2
Refinement stepCycle: final / Resolution: 3→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20694 0 3 33 20730
Biso mean--71.8 63.04 -
Num. residues----2541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01921260
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219798
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.95628818
X-RAY DIFFRACTIONr_angle_other_deg0.849345639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94652528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67623.3521047
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.986153585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.94915150
X-RAY DIFFRACTIONr_chiral_restr0.0680.23052
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02123857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025091
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 382 -
Rwork0.362 7243 -
all-7625 -
obs--99.97 %

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