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- PDB-4e36: Crystal structure of the human Endoplasmic Reticulum Aminopeptida... -

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Basic information

Entry
Database: PDB / ID: 4.0E+36
TitleCrystal structure of the human Endoplasmic Reticulum Aminopeptidase 2 variant N392K
ComponentsEndoplasmic reticulum aminopeptidase 2
KeywordsHYDROLASE / Thermolysin-like catalytic domain / Aminopeptidase / Zinc binding / Glycosylation / Endoplasmic Reticulum
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 / extracellular space / zinc ion binding / membrane / 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
LYSINE / Endoplasmic reticulum aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 3.22 Å
AuthorsBirtley, J.R. / Saridakis, E. / Pegias, P. / Stratikos, E. / Mavridis, I.M.
CitationJournal: J.Immunol. / Year: 2012
Title: A common single nucleotide polymorphism in endoplasmic reticulum aminopeptidase 2 induces a specificity switch that leads to altered antigen processing.
Authors: Evnouchidou, I. / Birtley, J. / Seregin, S. / Papakyriakou, A. / Zervoudi, E. / Samiotaki, M. / Panayotou, G. / Giastas, P. / Petrakis, O. / Georgiadis, D. / Amalfitano, A. / Saridakis, E. / ...Authors: Evnouchidou, I. / Birtley, J. / Seregin, S. / Papakyriakou, A. / Zervoudi, E. / Samiotaki, M. / Panayotou, G. / Giastas, P. / Petrakis, O. / Georgiadis, D. / Amalfitano, A. / Saridakis, E. / Mavridis, I.M. / Stratikos, E.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: 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_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 13, 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)226,78316
Polymers223,0612
Non-polymers3,72214
Water1,910106
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A: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4519
Polymers111,5301
Non-polymers1,9208
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3337
Polymers111,5301
Non-polymers1,8026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.340, 134.450, 127.370
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 61:125 or resseq 134:500 or resseq...
211chain B and (resseq 61:125 or resseq 134:500 or resseq...

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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, Irap, 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, 8 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
#5: 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.: 4
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, 112 molecules

#4: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE DISCREPANCY BETWEEN THE UNIPPROT ENTRY AND THE PROVIDED SEQUENCE AT RESIDUE 2 CORRESPONDS TO A ...THE DISCREPANCY BETWEEN THE UNIPPROT ENTRY AND THE PROVIDED SEQUENCE AT RESIDUE 2 CORRESPONDS TO A COMMON CLONING ARTIFACT.

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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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 8000, 20% ethylene glycol, 20 mM glycine, 20 mM DL-lysine, 20 mM DL-serine, 20 mM DL-alanine, 20 mM sodium L-glutamate, 31 mM imidazole, 69 mM MES. Protein mixed 1:4 with LPL ...Details: 10% PEG 8000, 20% ethylene glycol, 20 mM glycine, 20 mM DL-lysine, 20 mM DL-serine, 20 mM DL-alanine, 20 mM sodium L-glutamate, 31 mM imidazole, 69 mM MES. Protein mixed 1:4 with LPL peptide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Dec 4, 2011
RadiationMonochromator: BARTELS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.22→59.45 Å / Num. obs: 71589 / % possible obs: 99.1 % / Observed criterion σ(I): -5
Reflection shellResolution: 3.22→3.39 Å / % possible all: 99.39

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: isomorphous replacement
Starting model: PDB ENTRY 3SE6

3se6


Resolution: 3.22→10.996 Å / σ(F): 1.12 / Phase error: 28.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2608 3912 5.62 %
Rwork0.2087 --
obs0.2113 69634 89.42 %
all-77873 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.818 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1882 Å2-0 Å215.2206 Å2
2---15.5805 Å2-0 Å2
3---6.3347 Å2
Refinement stepCycle: LAST / Resolution: 3.22→10.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13985 0 236 106 14327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714600
X-RAY DIFFRACTIONf_angle_d1.1219779
X-RAY DIFFRACTIONf_dihedral_angle_d19.5055307
X-RAY DIFFRACTIONf_chiral_restr0.0652227
X-RAY DIFFRACTIONf_plane_restr0.0042450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A6804X-RAY DIFFRACTIONPOSITIONAL
12B6804X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.27410.37211470.27873443X-RAY DIFFRACTION98
3.2741-3.3320.3351540.27483406X-RAY DIFFRACTION98
3.332-3.39430.34431720.28023442X-RAY DIFFRACTION98
3.3943-3.46140.30131760.25453366X-RAY DIFFRACTION98
3.4614-3.53430.30762060.25913382X-RAY DIFFRACTION98
3.5343-3.61360.32611860.24023283X-RAY DIFFRACTION98
3.6136-3.70060.34261870.23693331X-RAY DIFFRACTION98
3.7006-3.79670.26791690.21873237X-RAY DIFFRACTION98
3.7967-3.90360.25231760.22273224X-RAY DIFFRACTION98
3.9036-4.02360.25091750.22292962X-RAY DIFFRACTION98
4.0236-4.15990.29291700.21573035X-RAY DIFFRACTION98
4.1599-4.31670.28031440.19863227X-RAY DIFFRACTION98
4.3167-4.50030.24251430.18773336X-RAY DIFFRACTION98
4.5003-4.71970.25461880.19243481X-RAY DIFFRACTION98
4.7197-4.98920.21731830.18253430X-RAY DIFFRACTION98
4.9892-5.33330.25521990.19683343X-RAY DIFFRACTION98
5.3333-5.79750.27661550.20193412X-RAY DIFFRACTION98
5.7975-6.48190.22791660.21563376X-RAY DIFFRACTION98
6.4819-7.67490.251650.18883151X-RAY DIFFRACTION98
7.6749-10.99650.17382090.14663297X-RAY DIFFRACTION98

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