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- PDB-3se6: Crystal structure of the human Endoplasmic Reticulum Aminopeptidase 2 -

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Basic information

Entry
Database: PDB / ID: 3se6
TitleCrystal structure of the human Endoplasmic Reticulum Aminopeptidase 2
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 / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsBirtley, J.R. / Saridakis, E. / Stratikos, E. / Mavridis, I.M.
CitationJournal: Biochemistry / Year: 2012
Title: The crystal structure of human endoplasmic reticulum aminopeptidase 2 reveals the atomic basis for distinct roles in antigen processing.
Authors: Birtley, J.R. / Saridakis, E. / Stratikos, E. / Mavridis, I.M.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Advisory / Structure summary
Category: audit_author / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact
Item: _audit_author.name / _pdbx_validate_close_contact.auth_atom_id_1 ..._audit_author.name / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
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 / database_PDB_caveat / diffrn_source / 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_chiral / 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.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _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_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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

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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)226,10814
Polymers223,0312
Non-polymers3,07712
Water2,270126
1
A: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2148
Polymers111,5151
Non-polymers1,6997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8936
Polymers111,5151
Non-polymers1,3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.579, 134.362, 128.009
Angle α, β, γ (deg.)90.00, 90.71, 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: 111515.375 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, 6 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.: 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
#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)][b-D-Manp]{[(4+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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, 132 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#7: 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
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNATURAL VARIANT AS DESCRIBED IN THE UNP ENTRY Q6P179

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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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 8000, 20% ethylene glycol, 61 mM MES, 39 mM imidazole, 20 mM sodium-L-glutamate, 20 mM D-L-alanine, 20 mM glycine, 20 mM D-L-lysine, 20 mM D-L-serine, pH 6.5, VAPOR DIFFUSION, ...Details: 10% PEG 8000, 20% ethylene glycol, 61 mM MES, 39 mM imidazole, 20 mM sodium-L-glutamate, 20 mM D-L-alanine, 20 mM glycine, 20 mM D-L-lysine, 20 mM D-L-serine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 15, 2011
RadiationMonochromator: Si 111 HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.99→19.9 Å / Num. all: 51080 / Num. obs: 50371 / % possible obs: 98.6 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.99→3.1 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→10.997 Å / σ(F): 0.04 / Phase error: 29.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.277 2297 5.33 %
Rwork0.2122 --
obs0.2155 43110 94.33 %
all-50008 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.42 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.1515 Å2-0 Å213.8704 Å2
2---13.2552 Å2-0 Å2
3---3.5061 Å2
Refinement stepCycle: LAST / Resolution: 3.08→10.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14014 0 194 126 14334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814584
X-RAY DIFFRACTIONf_angle_d1.19919755
X-RAY DIFFRACTIONf_dihedral_angle_d19.7565304
X-RAY DIFFRACTIONf_chiral_restr0.0712216
X-RAY DIFFRACTIONf_plane_restr0.0052454
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A6834X-RAY DIFFRACTIONPOSITIONAL
12B6834X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.13190.402890.28661813X-RAY DIFFRACTION98
3.1319-3.18750.4054900.28491850X-RAY DIFFRACTION98
3.1875-3.24730.38011000.27431912X-RAY DIFFRACTION98
3.2473-3.31180.3066940.26911870X-RAY DIFFRACTION98
3.3118-3.38180.33471180.25541976X-RAY DIFFRACTION98
3.3818-3.45810.30271040.2581994X-RAY DIFFRACTION98
3.4581-3.54170.3121270.24642033X-RAY DIFFRACTION98
3.5417-3.63410.2921130.23372070X-RAY DIFFRACTION98
3.6341-3.7370.25881150.22712094X-RAY DIFFRACTION98
3.737-3.85260.30071200.22082067X-RAY DIFFRACTION98
3.8526-3.9840.31421170.22152061X-RAY DIFFRACTION98
3.984-4.13530.25621480.21682063X-RAY DIFFRACTION98
4.1353-4.31260.25561050.19832087X-RAY DIFFRACTION98
4.3126-4.52490.22681110.1872139X-RAY DIFFRACTION98
4.5249-4.78630.2304950.17832149X-RAY DIFFRACTION98
4.7863-5.12090.2452990.18922161X-RAY DIFFRACTION98
5.1209-5.57450.28381060.20152152X-RAY DIFFRACTION98
5.5745-6.24840.29081080.21522137X-RAY DIFFRACTION98
6.2484-7.44260.28141250.2022174X-RAY DIFFRACTION98
7.4426-10.99670.2007950.15842129X-RAY DIFFRACTION98

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