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- PDB-6t6r: Human endoplasmic reticulum aminopeptidase 1 (ERAP1) in complex w... -

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Basic information

Entry
Database: PDB / ID: 6t6r
TitleHuman endoplasmic reticulum aminopeptidase 1 (ERAP1) in complex with (4aR,5S,6R,8S,8aR)-5-(2-(Furan-3-yl)ethyl)-8-hydroxy-5,6,8a-trimethyl-3,4,4a,5,6,7,8,8a-octahydronaphthalene-1-carboxylic acid
ComponentsEndoplasmic reticulum aminopeptidase 1
KeywordsHYDROLASE / ERAP1 / Aminopeptidase
Function / homology
Function and homology information


interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / metalloexopeptidase activity / peptide catabolic process / regulation of innate immune response / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / metalloexopeptidase activity / peptide catabolic process / regulation of innate immune response / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / response to bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / positive regulation of angiogenesis / angiogenesis / adaptive immune response / endopeptidase activity / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol
Similarity search - Function
Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase ...Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
D-MALATE / Chem-MNZ / Endoplasmic reticulum aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.67 Å
AuthorsRowland, P.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Targeting the Regulatory Site of ER Aminopeptidase 1 Leads to the Discovery of a Natural Product Modulator of Antigen Presentation.
Authors: Liddle, J. / Hutchinson, J.P. / Kitchen, S. / Rowland, P. / Neu, M. / Cecconie, T. / Holmes, D.S. / Jones, E. / Korczynska, J. / Koumantou, D. / Lea, J.D. / Nickels, L. / Pemberton, M. / ...Authors: Liddle, J. / Hutchinson, J.P. / Kitchen, S. / Rowland, P. / Neu, M. / Cecconie, T. / Holmes, D.S. / Jones, E. / Korczynska, J. / Koumantou, D. / Lea, J.D. / Nickels, L. / Pemberton, M. / Phillipou, A. / Schneck, J.L. / Sheehan, H. / Tinworth, C.P. / Uings, I. / Wojno-Picon, J. / Young, R.J. / Stratikos, E.
History
DepositionOct 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,12723
Polymers105,3431
Non-polymers1,78322
Water17,024945
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint21 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.220, 140.260, 57.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endoplasmic reticulum aminopeptidase 1 / ARTS-1 / Adipocyte-derived leucine aminopeptidase / A-LAP / Aminopeptidase PILS / Puromycin- ...ARTS-1 / Adipocyte-derived leucine aminopeptidase / A-LAP / Aminopeptidase PILS / Puromycin-insensitive leucyl-specific aminopeptidase / PILS-AP / Type 1 tumor necrosis factor receptor shedding aminopeptidase regulator


Mass: 105343.398 Da / Num. of mol.: 1 / Mutation: N70Q N154Q N414Q N760Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 / Production host: unidentified baculovirus
References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 5 types, 967 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MNZ / (4~{a}~{R},5~{S},6~{R},8~{S},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-8-oxidanyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid


Mass: 332.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 945 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PACT condition D1 (0.1M MMT, pH 4.0, 25% PEG 1500), MMT = DL-malic acid, MES monohydrate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.67→59.61 Å / Num. obs: 107621 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.7
Reflection shellResolution: 1.67→1.71 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 51056 / CC1/2: 0.474 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.67→24.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.088
RfactorNum. reflection% reflectionSelection details
Rfree0.194 5364 4.99 %RANDOM
Rwork0.169 ---
obs0.17 107497 99.9 %-
Displacement parametersBiso max: 122.99 Å2 / Biso mean: 31.03 Å2 / Biso min: 13.84 Å2
Baniso -1Baniso -2Baniso -3
1--3.3908 Å20 Å20 Å2
2--2.0326 Å20 Å2
3---1.3582 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.67→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 115 945 7973
Biso mean--41.78 46.94 -
Num. residues----856
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2512SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes171HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1027HARMONIC5
X-RAY DIFFRACTIONt_it7201HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion921SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9313SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7201HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9734HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion15.41
LS refinement shellResolution: 1.67→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2261 390 5.01 %
Rwork0.2338 7394 -
all0.2334 7784 -
obs--99.05 %
Refinement TLS params.Method: refined / Origin x: 31.2171 Å / Origin y: 32.3867 Å / Origin z: 12.6826 Å
111213212223313233
T-0.042 Å20.0074 Å20.0026 Å2--0.043 Å20.0072 Å2---0.0765 Å2
L0.3793 °20.2347 °2-0.1087 °2-0.4488 °2-0.1077 °2--0.3842 °2
S-0.0005 Å °-0.0155 Å °-0.0174 Å °-0.038 Å °-0.0169 Å °0.0183 Å °0.0467 Å °-0.0004 Å °0.0174 Å °
Refinement TLS groupSelection details: { A|* }

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