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- PDB-5j5e: crystal structure of antigen-ERAP1 domain complex -

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Basic information

Entry
Database: PDB / ID: 5j5e
Titlecrystal structure of antigen-ERAP1 domain complex
ComponentsEndoplasmic reticulum aminopeptidase 1ERAP1
KeywordsHYDROLASE / AMINOPEPTIDASE
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 / regulation of innate immune response / peptide catabolic process / 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 / regulation of innate immune response / peptide catabolic process / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / aminopeptidase activity / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / 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
Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain ...Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / 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. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endoplasmic reticulum aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSui, L. / Gandhi, A. / Guo, H.-C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI068831 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI078134 United States
Citation
Journal: Mol.Immunol. / Year: 2016
Title: Crystal structure of a polypeptide's C-terminus in complex with the regulatory domain of ER aminopeptidase 1.
Authors: Sui, L. / Gandhi, A. / Guo, H.C.
#1: Journal: Sci Rep / Year: 2011
Title: Structural insights into the molecular ruler mechanism of the endoplasmic reticulum aminopeptidase ERAP1.
Authors: Gandhi, A. / Lakshminarasimhan, D. / Sun, Y. / Guo, H.-C.
History
DepositionApr 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence / Refinement description
Category: pdbx_audit_support / pdbx_database_PDB_obs_spr / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 19, 2021Group: Database references / Category: citation / citation_author
Revision 1.4Apr 27, 2022Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)48,7461
Polymers48,7461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.260, 66.850, 66.500
Angle α, β, γ (deg.)90.00, 110.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoplasmic reticulum aminopeptidase 1 / ERAP1 / 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: 48745.914 Da / Num. of mol.: 1 / Fragment: unp residues 529-941
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris, pH 8.5 and 16% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→62.43 Å / Num. obs: 10114 / % possible obs: 77 % / Redundancy: 2.4 % / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.3 / % possible all: 81.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
iMOSFLM7.2.0data reduction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RJO

3rjo


Resolution: 2.8→62.43 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.848 / SU B: 15.211 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 500 5.1 %RANDOM
Rwork0.2067 ---
obs0.20987 9400 75.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.12 Å2
2---0.48 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.8→62.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 0 0 3328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193405
X-RAY DIFFRACTIONr_bond_other_d0.0020.023280
X-RAY DIFFRACTIONr_angle_refined_deg1.611.954593
X-RAY DIFFRACTIONr_angle_other_deg1.02237533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0095404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65724.438160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23615636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.681518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023783
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
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_it1.6232.7651631
X-RAY DIFFRACTIONr_mcbond_other1.6222.7641630
X-RAY DIFFRACTIONr_mcangle_it2.7734.1392032
X-RAY DIFFRACTIONr_mcangle_other2.7724.142033
X-RAY DIFFRACTIONr_scbond_it1.5732.9251774
X-RAY DIFFRACTIONr_scbond_other1.5692.9251774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6974.3152561
X-RAY DIFFRACTIONr_long_range_B_refined4.2621.5833793
X-RAY DIFFRACTIONr_long_range_B_other4.25921.5883794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 39 -
Rwork0.25 722 -
obs--80.11 %

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