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- PDB-6ryf: High-resolution crystal structure of ERAP1 in complex with 15mer ... -

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Basic information

Entry
Database: PDB / ID: 6ryf
TitleHigh-resolution crystal structure of ERAP1 in complex with 15mer phosphinic peptide
Components
  • Endoplasmic reticulum aminopeptidase 1
  • PSE-ARG-ILE-GLN-ARG-ALA-PHE-VAL-THR-ILE
KeywordsHYDROLASE / endoplasmic reticulum aminopeptidase 1 / ERAP1 / antigen presentation
Function / homology
Function and homology information


interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / Synthesis and processing of ENV and VPU / evasion of host immune response / metalloexopeptidase activity / Alpha-defensins / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / regulation of innate immune response ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / Synthesis and processing of ENV and VPU / evasion of host immune response / metalloexopeptidase activity / Alpha-defensins / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / regulation of innate immune response / Dectin-2 family / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / Binding and entry of HIV virion / aminopeptidase activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide binding / Assembly Of The HIV Virion / Budding and maturation of HIV virion / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / positive regulation of angiogenesis / clathrin-dependent endocytosis of virus by host cell / angiogenesis / endopeptidase activity / adaptive immune response / viral protein processing / symbiont entry into host cell / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / endoplasmic reticulum membrane / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion 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 / tricorn interacting facor f3 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 / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / 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 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROPANOIC ACID / Envelope glycoprotein gp160 / Endoplasmic reticulum aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGiastas, P. / Stratikos, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1.
Authors: Giastas, P. / Mpakali, A. / Papakyriakou, A. / Lelis, A. / Kokkala, P. / Neu, M. / Rowland, P. / Liddle, J. / Georgiadis, D. / Stratikos, E.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 1
G: PSE-ARG-ILE-GLN-ARG-ALA-PHE-VAL-THR-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,08434
Polymers103,9762
Non-polymers3,10832
Water10,611589
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint20 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.693, 117.157, 146.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AG

#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: 102208.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Protein/peptide PSE-ARG-ILE-GLN-ARG-ALA-PHE-VAL-THR-ILE


Mass: 1767.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC PHOSPHINIC PSEUDOPEPTIDE / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS

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Sugars , 2 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 617 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM propionic acid, cacodylate and Bis-tris propane pH 7.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.72→91.52 Å / Num. obs: 106245 / % possible obs: 99.98 % / Redundancy: 8 % / CC1/2: 0.999 / Net I/σ(I): 12.5
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 5264 / CC1/2: 0.368 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YD0

2yd0


Resolution: 1.72→91.52 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.42
RfactorNum. reflection% reflection
Rfree0.2013 1498 1.41 %
Rwork0.1765 --
obs0.1768 106232 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→91.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7056 0 113 589 7758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077441
X-RAY DIFFRACTIONf_angle_d0.87410078
X-RAY DIFFRACTIONf_dihedral_angle_d3.4176039
X-RAY DIFFRACTIONf_chiral_restr0.0521138
X-RAY DIFFRACTIONf_plane_restr0.0061252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.77550.31671350.30719411X-RAY DIFFRACTION100
1.7755-1.8390.31111350.27759410X-RAY DIFFRACTION100
1.839-1.91260.26871340.24659409X-RAY DIFFRACTION100
1.9126-1.99970.24741340.22339425X-RAY DIFFRACTION100
1.9997-2.10510.22571360.20289444X-RAY DIFFRACTION100
2.1051-2.2370.25531350.18929458X-RAY DIFFRACTION100
2.237-2.40970.18471360.17569492X-RAY DIFFRACTION100
2.4097-2.65230.19861360.17089520X-RAY DIFFRACTION100
2.6523-3.03610.21941360.17069565X-RAY DIFFRACTION100
3.0361-3.82520.16341390.15299628X-RAY DIFFRACTION100
3.8252-91.6510.18111420.15939972X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2278-0.46090.57271.4654-1.09111.78320.24710.2487-0.012-0.4579-0.17360.03460.29550.1408-0.0480.31760.09780.0060.2124-0.01390.1742-619.7458379.2034442.8511
21.1192-0.64820.52650.7354-0.17921.52850.10140.01130.06-0.0892-0.1089-0.10230.0148-0.0385-0.00020.15180.0096-0.00070.18690.03880.2686-601.4218369.204473.0697
30.7794-0.05930.00931.5899-0.42450.5111-0.0053-0.08850.07420.04580.06570.1592-0.084-0.0126-0.05620.17010.00090.01860.2437-0.01060.2418-627.2385388.6869473.3027
43.7690.21940.09222.5565-3.03524.30240.0818-0.43280.27940.5143-0.0060.4837-0.3557-0.29820.00670.49340.08660.01980.4066-0.04320.2867-619.7204381.3758456.4322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 452 )
2X-RAY DIFFRACTION2chain 'A' and (resid 453 through 669 )
3X-RAY DIFFRACTION3chain 'A' and (resid 670 through 936 )
4X-RAY DIFFRACTION4chain 'G' and (resid 1 through 14 )

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