[English] 日本語
Yorodumi
- PDB-6ryf: High-resolution crystal structure of ERAP1 in complex with 15mer ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ryf
TitleHigh-resolution crystal structure of ERAP1 in complex with 15mer phosphinic peptide
Components
  • Endoplasmic reticulum aminopeptidase 1ERAP1
  • 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 / antigen processing and presentation of peptide antigen via MHC class I / Alpha-defensins / 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 / antigen processing and presentation of peptide antigen via MHC class I / Alpha-defensins / peptide catabolic process / regulation of innate immune response / fat cell differentiation / Dectin-2 family / 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 / peptide binding / response to bacterium / 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 / virus-mediated perturbation of host defense response / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host endosome membrane / viral envelope / endoplasmic reticulum membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

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

#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: 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

-
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 / N-Acetylglucosamine


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

-
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 / Bis-tris propane


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 / 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 / Propionic acid


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


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more