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Basic information

Entry
Database: PDB / ID: 4jbs
TitleCrystal structure of the human Endoplasmic Reticulum Aminopeptidase 2 in complex with PHOSPHINIC PSEUDOTRIPEPTIDE inhibitor.
ComponentsEndoplasmic reticulum aminopeptidase 2
KeywordsHydrolase/Hydrolase Inhibitor / Thermolysin-like catalytic domain / Hydrolase / Aminopeptidase / Zinc binding / Endoplasmic Reticulum / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / 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 / metallopeptidase activity ...Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / 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 / metallopeptidase activity / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / proteolysis / zinc ion binding / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / Chem-P52 / Endoplasmic reticulum aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.789 Å
AuthorsSaridakis, E. / Birtley, J. / Stratikos, E. / Mavridis, I.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Rationally designed inhibitor targeting antigen-trimming aminopeptidases enhances antigen presentation and cytotoxic T-cell responses.
Authors: Zervoudi, E. / Saridakis, E. / Birtley, J.R. / Seregin, S.S. / Reeves, E. / Kokkala, P. / Aldhamen, Y.A. / Amalfitano, A. / Mavridis, I.M. / James, E. / Georgiadis, D. / Stratikos, E.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)227,48317
Polymers223,0612
Non-polymers4,42215
Water5,278293
1
A: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,75910
Polymers111,5301
Non-polymers2,2299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7247
Polymers111,5301
Non-polymers2,1936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.150, 134.770, 128.731
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 111530.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP2, LRAP / Plasmid: pFASTBac-1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q6P179, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Sugars , 3 types, 9 molecules

#2: 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.: 3
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
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-alpha-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 5
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 , 4 types, 299 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-P52 / Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide


Mass: 512.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37N4O4P
#7: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 8000, 20% ethylene glycol, 69 mM MES, 31 mM imidazole.Drops incubated at 277 K before being transferred to 289 K, pH 6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 25, 2012
RadiationMonochromator: BARTELS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.789→49 Å / Num. all: 125739 / Num. obs: 119216 / % possible obs: 94.81 % / Observed criterion σ(I): -5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E36

4e36


Resolution: 2.789→10.994 Å / σ(F): 0.62 / Phase error: 31.58 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2778 6294 5.37 %
Rwork0.2064 --
obs0.21 117190 94.73 %
all-123709 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.057 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0067 Å2-0 Å26.9545 Å2
2---6.9397 Å2-0 Å2
3---2.1171 Å2
Refinement stepCycle: LAST / Resolution: 2.789→10.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13862 0 288 293 14443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814537
X-RAY DIFFRACTIONf_angle_d0.87219706
X-RAY DIFFRACTIONf_dihedral_angle_d18.3195246
X-RAY DIFFRACTIONf_chiral_restr0.0582218
X-RAY DIFFRACTIONf_plane_restr0.0032434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7895-2.83680.423240.33735453X-RAY DIFFRACTION98
2.8368-2.88740.37542880.3395708X-RAY DIFFRACTION98
2.8874-2.94190.40282940.32135545X-RAY DIFFRACTION98
2.9419-3.00080.35193130.30195667X-RAY DIFFRACTION98
3.0008-3.06470.31342590.30165482X-RAY DIFFRACTION98
3.0647-3.13430.39492590.28255592X-RAY DIFFRACTION98
3.1343-3.21080.37033080.27625460X-RAY DIFFRACTION98
3.2108-3.29540.30283120.26735420X-RAY DIFFRACTION98
3.2954-3.38960.33072890.25455197X-RAY DIFFRACTION98
3.3896-3.49560.33082910.23765215X-RAY DIFFRACTION98
3.4956-3.61620.31823020.23215549X-RAY DIFFRACTION98
3.6162-3.75550.31853100.20885653X-RAY DIFFRACTION98
3.7555-3.9190.24892750.20435746X-RAY DIFFRACTION98
3.919-4.11530.24533200.19095790X-RAY DIFFRACTION98
4.1153-4.3580.24153190.17215711X-RAY DIFFRACTION98
4.358-4.67040.22962920.15595712X-RAY DIFFRACTION98
4.6704-5.09730.21742990.15715565X-RAY DIFFRACTION98
5.0973-5.74120.2573060.17385616X-RAY DIFFRACTION98
5.7412-6.91940.27322760.18945301X-RAY DIFFRACTION98
6.9194-10.99410.21443270.14145845X-RAY DIFFRACTION98

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