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- PDB-4z7i: Crystal structure of insulin regulated aminopeptidase in complex ... -

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Basic information

Entry
Database: PDB / ID: 4z7i
TitleCrystal structure of insulin regulated aminopeptidase in complex with ligand
Components
  • DG025 transition-state analogue enzyme inhibitor
  • Leucyl-cystinyl aminopeptidase
KeywordsHYDROLASE / aminopeptidase / antigen presentation / transition-state analogue / enzyme inhibitor / IRAP
Function / homology
Function and homology information


cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / peptide binding / cytoplasmic vesicle membrane / early endosome lumen / Endosomal/Vacuolar pathway ...cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / peptide binding / cytoplasmic vesicle membrane / early endosome lumen / Endosomal/Vacuolar pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein catabolic process / female pregnancy / regulation of blood pressure / protein polyubiquitination / metallopeptidase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell-cell signaling / lysosomal membrane / perinuclear region of cytoplasm / proteolysis / extracellular space / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol
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 / 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 / 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 / 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
Leucyl-cystinyl aminopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsMpakali, A. / Saridakis, E. / Harlos, K. / Zhao, Y. / Stratikos, E.
Funding support Greece, 2items
OrganizationGrant numberCountry
General Secretariat for Research & TechnologyERC-14 Greece
European UnionFP7 BioStruct-X 283570
CitationJournal: J Immunol. / Year: 2015
Title: Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing.
Authors: Mpakali, A. / Saridakis, E. / Harlos, K. / Zhao, Y. / Papakyriakou, A. / Kokkala, P. / Georgiadis, D. / Stratikos, E.
History
DepositionApr 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_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.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 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucyl-cystinyl aminopeptidase
B: Leucyl-cystinyl aminopeptidase
C: DG025 transition-state analogue enzyme inhibitor
D: DG025 transition-state analogue enzyme inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,28627
Polymers211,1294
Non-polymers6,15723
Water25214
1
A: Leucyl-cystinyl aminopeptidase
C: DG025 transition-state analogue enzyme inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,03814
Polymers105,5642
Non-polymers3,47412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-1 kcal/mol
Surface area36730 Å2
MethodPISA
2
B: Leucyl-cystinyl aminopeptidase
D: DG025 transition-state analogue enzyme inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,24813
Polymers105,5642
Non-polymers2,68411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-3 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.520, 256.350, 73.060
Angle α, β, γ (deg.)90.00, 111.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Leucyl-cystinyl aminopeptidase / Cystinyl aminopeptidase / Insulin-regulated membrane aminopeptidase / Insulin-responsive ...Cystinyl aminopeptidase / Insulin-regulated membrane aminopeptidase / Insulin-responsive aminopeptidase / IRAP / Oxytocinase / OTase / Placental leucine aminopeptidase / P-LAP


Mass: 104234.805 Da / Num. of mol.: 2 / Fragment: UNP residues 155-1025
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNPEP, OTASE / Production host: Homo sapiens (human) / References: UniProt: Q9UIQ6, cystinyl aminopeptidase
#2: Protein/peptide DG025 transition-state analogue enzyme inhibitor


Mass: 1329.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 21 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.: 5
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 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 15
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 , 2 types, 16 molecules

#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG 20000, 20% PEG 500 monomethyl ether, 0.2 M D-glucose, 0.2M D-mannose, 0.2M D-galactose, 0.2M L-fucose, 0.2M D-xylose, 0.2M N-acetyl-D-glucosamine, bicine, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.31→128.2 Å / Num. obs: 34796 / % possible obs: 99.9 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.1
Reflection shellResolution: 3.31→3.4 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P8Q

4p8q


Resolution: 3.31→128.18 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1676 4.82 %Random selection
Rwork0.211 ---
obs0.214 34758 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.31→128.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13953 0 391 14 14358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414717
X-RAY DIFFRACTIONf_angle_d0.99119972
X-RAY DIFFRACTIONf_dihedral_angle_d16.6135252
X-RAY DIFFRACTIONf_chiral_restr0.0412292
X-RAY DIFFRACTIONf_plane_restr0.0042468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.40740.36331590.29552734X-RAY DIFFRACTION100
3.4074-3.51740.37641100.26562754X-RAY DIFFRACTION100
3.5174-3.64320.34761190.25622804X-RAY DIFFRACTION100
3.6432-3.7890.33071200.25552775X-RAY DIFFRACTION100
3.789-3.96150.30681390.24742717X-RAY DIFFRACTION100
3.9615-4.17040.31281320.22052764X-RAY DIFFRACTION100
4.1704-4.43160.27531630.21222750X-RAY DIFFRACTION100
4.4316-4.77380.23921520.20832716X-RAY DIFFRACTION100
4.7738-5.25430.27811530.20412777X-RAY DIFFRACTION100
5.2543-6.01450.32211350.22392744X-RAY DIFFRACTION100
6.0145-7.57760.25061430.21792776X-RAY DIFFRACTION100
7.5776-128.27110.21871510.1742771X-RAY DIFFRACTION100

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