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- PDB-7mwb: ERAP1 binds peptide C-terminus of a SPF sequence (FKARKF) -

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Basic information

Entry
Database: PDB / ID: 7mwb
TitleERAP1 binds peptide C-terminus of a SPF sequence (FKARKF)
ComponentsEndoplasmic reticulum aminopeptidase 1,SPF Sequence
KeywordsHYDROLASE / Antigen presentation / ERAP1 molecular ruler mechanism
Function / homology
Function and homology information


interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / 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 / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / 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 / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal 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 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Endoplasmic reticulum aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGuo, H.C. / Sui, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128152-01 United States
CitationJournal: Immunobiology / Year: 2021
Title: ERAP1 binds peptide C-termini of different sequences and/or lengths by a common recognition mechanism.
Authors: Sui, L. / Guo, H.C.
History
DepositionMay 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 1,SPF Sequence
B: Endoplasmic reticulum aminopeptidase 1,SPF Sequence
C: Endoplasmic reticulum aminopeptidase 1,SPF Sequence
D: Endoplasmic reticulum aminopeptidase 1,SPF Sequence


Theoretical massNumber of molelcules
Total (without water)194,6714
Polymers194,6714
Non-polymers00
Water1,51384
1
A: Endoplasmic reticulum aminopeptidase 1,SPF Sequence
D: Endoplasmic reticulum aminopeptidase 1,SPF Sequence


Theoretical massNumber of molelcules
Total (without water)97,3362
Polymers97,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum aminopeptidase 1,SPF Sequence
C: Endoplasmic reticulum aminopeptidase 1,SPF Sequence


Theoretical massNumber of molelcules
Total (without water)97,3362
Polymers97,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.430, 69.980, 121.240
Angle α, β, γ (deg.)90.110, 100.870, 90.150
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.364028, 0.08576, -0.927431), (-0.034584, -0.99631, -0.078555), (-0.930746, 0.003478, 0.36565)147.70956, 35.91192, 53.39522
3given(0.364406, 0.085087, 0.927345), (0.035782, -0.996361, 0.077358), (0.930553, 0.004992, -0.366124)-26.6245, 53.97108, -48.07224
4given(-0.999992, -0.00369, -0.001491), (-0.003693, 0.999991, 0.002005), (0.001483, 0.002011, -0.999997)125.33235, -33.16573, 3.92606

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Components

#1: Protein
Endoplasmic reticulum aminopeptidase 1,SPF Sequence / 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: 48667.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A few residues are missing or truncated to the beta carbon, due to poor local density
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases, EC: 3.4.1.1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidues 529-941 are from ERAP1. Residues 942-947 constitute the designed SPF sequence used in this construct.

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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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris, pH 8.5, 12% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→60.4 Å / Num. obs: 31140 / % possible obs: 96 % / Redundancy: 2.3 % / Rsym value: 0.124 / Net I/σ(I): 3.7
Reflection shellResolution: 3.2→3.4 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4376 / Rsym value: 0.232 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
pointlessdata scaling
Aimlessdata scaling
iMOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RJO

3rjo


Resolution: 3.2→59.51 Å / Cor.coef. Fo:Fc: 0.81 / Cor.coef. Fo:Fc free: 0.686 / SU B: 59.907 / SU ML: 0.944 / Cross valid method: THROUGHOUT / σ(F): 1.96 / ESU R Free: 0.805 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1583 5.3 %RANDOM
Rwork0.271 ---
obs0.276 28320 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.61 Å2 / Biso mean: 29.87 Å2 / Biso min: 6.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20.02 Å24.99 Å2
2---2.32 Å20.76 Å2
3----2.38 Å2
Refinement stepCycle: final / Resolution: 3.2→59.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13289 0 0 84 13373
Biso mean---20.92 -
Num. residues----1628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01313581
X-RAY DIFFRACTIONr_bond_other_d0.0350.01712706
X-RAY DIFFRACTIONr_angle_refined_deg1.641.63618313
X-RAY DIFFRACTIONr_angle_other_deg2.2281.57529458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.57151609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93922.717714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.723152532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1831576
X-RAY DIFFRACTIONr_chiral_restr0.1110.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214848
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022924
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 119 -
Rwork0.349 2108 -
all-2227 -
obs--95.83 %

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