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- PDB-6eot: DPP8 - SLRFLYEG, space group 19 -

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Basic information

Entry
Database: PDB / ID: 6eot
TitleDPP8 - SLRFLYEG, space group 19
Components
  • Dipeptidyl peptidase 8
  • SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
KeywordsHYDROLASE / DPP8
Function / homology
Function and homology information


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 / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding ...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 / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / dipeptidyl-peptidase IV / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / dipeptidyl-peptidase activity / negative regulation of programmed cell death / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / negative regulation of DNA binding / ubiquitin-like protein ligase 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 / nuclear pore / Regulation of IFNG signaling / aminopeptidase activity / cellular response to cadmium ion / serine-type peptidase activity / 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 / protein tag activity / Formation of Incision Complex in GG-NER / 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 / protein stabilization / nuclear body / nuclear speck / immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / nucleolus / 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 / Ubiquitin homologues ...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-like domain / Ubiquitin domain profile. / 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: 3.5 Å
AuthorsRoss, B.R. / Huber, R.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer.
Authors: Ross, B. / Krapp, S. / Augustin, M. / Kierfersauer, R. / Arciniega, M. / Geiss-Friedlander, R. / Huber, R.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 9, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.4Jan 17, 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
F: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
B: Dipeptidyl peptidase 8
C: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
D: Dipeptidyl peptidase 8
E: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
G: Dipeptidyl peptidase 8
H: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
I: Dipeptidyl peptidase 8
J: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
K: Dipeptidyl peptidase 8
L: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY


Theoretical massNumber of molelcules
Total (without water)626,81112
Polymers626,81112
Non-polymers00
Water59433
1
A: Dipeptidyl peptidase 8
F: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
B: Dipeptidyl peptidase 8
C: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY


Theoretical massNumber of molelcules
Total (without water)208,9374
Polymers208,9374
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-34 kcal/mol
Surface area63740 Å2
MethodPISA
2
D: Dipeptidyl peptidase 8
E: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
G: Dipeptidyl peptidase 8
H: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY


Theoretical massNumber of molelcules
Total (without water)208,9374
Polymers208,9374
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-32 kcal/mol
Surface area64210 Å2
MethodPISA
3
I: Dipeptidyl peptidase 8
J: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
K: Dipeptidyl peptidase 8
L: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY


Theoretical massNumber of molelcules
Total (without water)208,9374
Polymers208,9374
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-32 kcal/mol
Surface area63630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.159, 264.675, 268.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 103483.352 Da / Num. of mol.: 6
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-TYR-GLU-GLY


Mass: 985.116 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P63165*PLUS
#3: Water ChemComp-HOH / water / Water


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

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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: 4.21 Å3/Da / Density % sol: 70.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Na citrate 0.46M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 3.5→43.8 Å / Num. obs: 133413 / % possible obs: 99.9 % / Redundancy: 8.39 % / Rsym value: 0.35 / Net I/σ(I): 6.8
Reflection shellResolution: 3.5→3.72 Å / Redundancy: 8.47 % / Mean I/σ(I) obs: 2.58 / Num. unique obs: 22513 / CC1/2: 0.74 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ORV

1orv


Resolution: 3.5→43.87 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.856 / SU B: 30.447 / SU ML: 0.442 / Cross valid method: THROUGHOUT / ESU R Free: 0.532 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26205 6671 5 %RANDOM
Rwork0.20513 ---
obs0.20793 126742 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.258 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å20 Å2
2--0.08 Å2-0 Å2
3----2.75 Å2
Refinement stepCycle: 1 / Resolution: 3.5→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41090 0 0 33 41123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01942213
X-RAY DIFFRACTIONr_bond_other_d0.0020.0239304
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.95757231
X-RAY DIFFRACTIONr_angle_other_deg0.909390615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70155014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09723.3832078
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86157108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.40715294
X-RAY DIFFRACTIONr_chiral_restr0.0750.26071
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02147327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210079
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_it2.777.17320146
X-RAY DIFFRACTIONr_mcbond_other2.777.17320145
X-RAY DIFFRACTIONr_mcangle_it4.66110.75525130
X-RAY DIFFRACTIONr_mcangle_other4.66110.75525131
X-RAY DIFFRACTIONr_scbond_it2.3477.35722067
X-RAY DIFFRACTIONr_scbond_other2.3477.35722068
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.13310.9532102
X-RAY DIFFRACTIONr_long_range_B_refined6.87281.14145887
X-RAY DIFFRACTIONr_long_range_B_other6.87281.14245888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 483 -
Rwork0.315 9185 -
obs--99.45 %

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