[English] 日本語
Yorodumi
- PDB-7nup: Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nup
TitleEndoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand
ComponentsEndoplasmic reticulum aminopeptidase 2
KeywordsHYDROLASE / Hydroxamic inhibitor / complex / aminopeptidase / Zinc containing enzyme
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / antigen processing and presentation of peptide antigen via MHC class I / metalloaminopeptidase activity / aminopeptidase activity / peptide binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity ...Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / antigen processing and presentation of peptide antigen via MHC class I / metalloaminopeptidase activity / aminopeptidase activity / peptide binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / proteolysis / extracellular space / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal 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 ...Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal 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 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
BROMIDE ION / TRIETHYLENE GLYCOL / Chem-USK / Endoplasmic reticulum aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMpakali, A. / Giastas, P. / Stratikos, E.
CitationJournal: To Be Published
Title: Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand
Authors: Mpakali, A. / Giastas, P. / Stratikos, E.
History
DepositionMar 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 2
B: Endoplasmic reticulum aminopeptidase 2
C: Endoplasmic reticulum aminopeptidase 2
D: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)461,30261
Polymers445,7014
Non-polymers15,60157
Water1,928107
1
A: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,78022
Polymers111,4251
Non-polymers4,35521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,76015
Polymers111,4251
Non-polymers4,33514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,97112
Polymers111,4251
Non-polymers3,54511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,79112
Polymers111,4251
Non-polymers3,36511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.273, 127.186, 133.412
Angle α, β, γ (deg.)90.920, 90.080, 90.870
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Endoplasmic reticulum aminopeptidase 2 / Leukocyte-derived arginine aminopeptidase / L-RAP


Mass: 111425.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP2, LRAP / Cell line (production host): Sf21
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q6P179, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

-
Sugars , 5 types, 32 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 8
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
#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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.: 17 / Source method: obtained synthetically / 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, 132 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-USK / (3~{S})-4-(4-hydroxyphenyl)-~{N}-oxidanyl-3-[5-[[(5-phenylthiophen-2-yl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]butanamide


Mass: 513.589 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H23N5O5S2
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Br
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03M of each halide (sodium fluoride, sodium bromide, sodium iodide), 0.1M MES/imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.664 Å / Num. obs: 73659 / % possible obs: 83.24 % / Redundancy: 3.2 % / CC1/2: 0.921 / Net I/σ(I): 1.6
Reflection shellResolution: 3.1→3.142 Å / Num. unique obs: 1151 / CC1/2: 0.6 / % possible all: 35

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AB0

5ab0


Resolution: 3.1→48.664 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2666 3482 4.73 %
Rwork0.1818 70177 -
obs0.1858 73659 83.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 354.84 Å2 / Biso mean: 56.5113 Å2 / Biso min: 1.77 Å2
Refinement stepCycle: final / Resolution: 3.1→48.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28861 0 958 107 29926
Biso mean--82.2 35.75 -
Num. residues----3589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.14250.3619690.2623115135
3.1425-3.18740.4223740.2749153845
3.1874-3.23490.47221080.31174052
3.2349-3.28550.41531250.2892227869
3.2855-3.33930.34531760.2468279082
3.3393-3.39690.3321770.2528300290
3.3969-3.45860.418590.275633857
3.4586-3.52520.33381350.2363290190
3.5252-3.59710.32161340.2155328098
3.5971-3.67530.30151040.2179264678
3.6753-3.76070.27041510.197336198
3.7607-3.85470.30321280.1997333097
3.8547-3.95890.31761170.1877205361
3.9589-4.07540.2951800.1729330399
4.0754-4.20680.251440.1581330598
4.2068-4.35710.24871920.148333399
4.3571-4.53140.21382260.1383326198
4.5314-4.73750.20311390.1385335199
4.7375-4.9870.20871240.1362338299
4.987-5.29910.21731230.1505341099
5.2991-5.70770.30092000.1761329099
5.7077-6.2810.28391570.1942331499
6.281-7.18740.26331410.1933332598
7.1874-9.04590.21581770.1596331798
9.0459-48.6640.20891720.1737317895
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)
11.2006-0.0239-0.01850.5855-0.25821.07840.0594-0.0102-0.102-0.1034-0.03470.09040.0715-0.155-0.02720.2212-0.0393-0.03730.1745-0.05810.212712.86080.5797-11.7232
21.75550.78180.49842.20580.4591.413-0.0491-0.273-0.58260.14290.0057-0.15870.42580.11510.01840.34530.0605-0.02230.31460.11250.410734.7978-19.460111.8379
31.38370.46040.13131.2197-0.50151.6109-0.0063-0.27920.21790.06860.04540.0285-0.04480.0591-0.03140.2464-0.0425-0.02620.3005-0.05630.211730.842112.750414.6021
41.7717-0.1002-0.82480.8065-0.15621.75930.1063-0.11810.1177-0.1051-0.0514-0.0833-0.09830.4345-0.05030.2138-0.052-0.01260.37230.00490.200461.9171-3.940654.8819
52.20510.942-0.88051.9256-0.43211.54420.2108-0.20790.59530.1282-0.03090.167-0.9758-0.2073-0.13020.670.04690.07730.3979-0.17980.513541.390818.727978.484
61.16130.3119-0.26581.45490.4371.91660.0769-0.1299-0.11640.1314-0.02810.0510.2063-0.0719-0.03120.2873-0.0565-0.01850.319-0.01240.196442.7569-14.867381.6918
71.8629-0.68-0.09782.54540.14720.8190.15690.33440.2249-0.4158-0.1525-0.389-0.14780.12950.01810.38620.0570.06830.27760.05790.297628.2481-75.1275-22.3295
81.3795-0.2577-0.10711.70780.15650.87380.3096-0.01390.64170.2711-0.01410.0338-0.2351-0.1607-0.20080.64220.04440.11130.25470.00250.694813.9836-49.5147-8.8997
90.91240.2275-0.27592.4296-0.48411.04250.0721-0.23640.24740.8630.10860.7037-0.4637-0.1208-0.08370.78370.02640.22590.4288-0.04640.56835.7473-66.69477.8264
102.5738-0.4896-0.29952.2226-0.98321.9472-0.00150.3197-0.2615-0.3261-0.00150.30390.1645-0.47720.02130.37340.0423-0.03350.4228-0.08050.270239.2933-54.948444.3093
112.0653-0.00790.81641.5094-0.20221.34580.1974-0.1757-1.0004-0.0539-0.0367-0.12230.49780.298-0.04560.54920.16930.0410.40150.12810.81865.1664-74.150855.4193
121.8211-0.29840.91311.3808-0.3271.4743-0.2453-0.5375-0.23290.33760.1373-0.2189-0.0033-0.02070.10950.50130.1004-0.02370.68610.16390.474171.9804-60.051675.3008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 500 )A49 - 500
2X-RAY DIFFRACTION2chain 'A' and (resid 501 through 712 )A501 - 712
3X-RAY DIFFRACTION3chain 'A' and (resid 713 through 963 )A713 - 963
4X-RAY DIFFRACTION4chain 'B' and (resid 51 through 500 )B51 - 500
5X-RAY DIFFRACTION5chain 'B' and (resid 501 through 672 )B501 - 672
6X-RAY DIFFRACTION6chain 'B' and (resid 673 through 962 )B673 - 962
7X-RAY DIFFRACTION7chain 'C' and (resid 52 through 385 )C52 - 385
8X-RAY DIFFRACTION8chain 'C' and (resid 386 through 605 )C386 - 605
9X-RAY DIFFRACTION9chain 'C' and (resid 606 through 960 )C606 - 960
10X-RAY DIFFRACTION10chain 'D' and (resid 51 through 271 )D51 - 271
11X-RAY DIFFRACTION11chain 'D' and (resid 272 through 638 )D272 - 638
12X-RAY DIFFRACTION12chain 'D' and (resid 639 through 962 )D639 - 962

+
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