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- PDB-3mdj: ER Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibi... -

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Basic information

Entry
Database: PDB / ID: 3mdj
TitleER Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin
ComponentsEndoplasmic reticulum aminopeptidase 1ERAP1
KeywordsHydrolase/Hydrolase Inhibitor / aminopeptidase / Zn binding protein / ER / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / regulation of innate immune response / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / regulation of innate immune response / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / positive regulation of angiogenesis / angiogenesis / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / cytosol / 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
Chem-BES / Endoplasmic reticulum aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsNguyen, T.T. / Stern, L.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1.
Authors: Nguyen, T.T. / Chang, S.C. / Evnouchidou, I. / York, I.A. / Zikos, C. / Rock, K.L. / Goldberg, A.L. / Stratikos, E. / Stern, L.J.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Other
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.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_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
Revision 2.1Sep 6, 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 / pdbx_unobs_or_zero_occ_residues
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 1
B: Endoplasmic reticulum aminopeptidase 1
C: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,74715
Polymers315,7163
Non-polymers4,03112
Water0
1
A: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9666
Polymers105,2391
Non-polymers1,7275
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2585
Polymers105,2391
Non-polymers1,0194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5234
Polymers105,2391
Non-polymers1,2853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.029, 234.635, 95.860
Angle α, β, γ (deg.)90.00, 103.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34
15
25
35

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 46:141) and (not element H) and (not element D)
211chain B and (resseq 46:141) and (not element H) and (not element D)
311chain C and (resseq 46:141) and (not element H) and (not element D)
112chain A and (resseq 142:501) and (not element H) and (not element D)
212chain B and (resseq 142:501) and (not element H) and (not element D)
312chain C and (resseq 142:501) and (not element H) and (not element D)
113chain A and (resseq 502:602) and (not element H) and (not element D)
213chain B and (resseq 502:602) and (not element H) and (not element D)
313chain C and (resseq 502:602) and (not element H) and (not element D)
114chain A and (resseq 603:698) and (not element H) and (not element D)
214chain B and (resseq 603:698) and (not element H) and (not element D)
314chain C and (resseq 603:698) and (not element H) and (not element D)
115Chain A and (resseq 699:934) and (not element H) and (not element D)
215Chain B and (resseq 699:934) and (not element H) and (not element D)
315Chain C and (resseq 699:934) and (not element H) and (not element D)

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(0.164122, 0.733748, 0.6593), (-0.491017, -0.518912, 0.699738), (0.85555, -0.43857, 0.275118)-39.560799, 155.830994, 12.1064
2given(0.163489, -0.544208, 0.822867), (0.695633, -0.527851, -0.487307), (0.699547, 0.652083, 0.292271)76.972099, 118.122002, -79.836502
3given(0.172178, 0.757168, 0.63012), (-0.502981, -0.482425, 0.717131), (0.846974, -0.440413, 0.297778)-43.049, 155.070007, 13.9694
4given(0.161326, -0.542051, 0.824715), (0.705216, -0.521276, -0.480563), (0.690394, 0.65913, 0.298168)76.669601, 117.655998, -80.460503
5given(0.199735, 0.722916, 0.661437), (-0.485558, -0.513304, 0.707639), (0.851081, -0.462506, 0.248493)-38.494801, 157.072998, 13.1282
6given(0.211666, -0.533237, 0.819058), (0.726886, -0.47432, -0.496646), (0.653325, 0.700485, 0.287206)76.562202, 112.463997, -85.9104
7given(0.200553, 0.749399, 0.631015), (-0.477745, -0.487513, 0.730815), (0.8553, -0.448031, 0.26025)-43.328701, 155.466995, 12.4299
8given(0.16507, -0.542775, 0.823497), (0.7146, -0.509658, -0.479162), (0.679779, 0.667566, 0.303738)76.503098, 116.343002, -81.447098
9given(0.212959, 0.759499, 0.614662), (-0.484244, -0.464351, 0.741543), (0.84862, -0.455565, 0.268895)-46.143002, 153.839005, 14.2162
10given(0.165219, -0.579134, 0.798315), (0.699512, -0.501802, -0.5088), (0.695259, 0.642494, 0.322204)81.3041, 115.008003, -77.9533

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Endoplasmic reticulum aminopeptidase 1 / ERAP1 / Adipocyte-derived leucine aminopeptidase / A-LAP / ARTS-1 / Aminopeptidase PILS / Puromycin- ...Adipocyte-derived leucine aminopeptidase / A-LAP / ARTS-1 / Aminopeptidase PILS / Puromycin-insensitive leucyl-specific aminopeptidase / PILS-AP / Type 1 tumor necrosis factor receptor shedding aminopeptidase regulator


Mass: 105238.734 Da / Num. of mol.: 3 / Fragment: UNP residues 37-939
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5
References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Sugars , 3 types, 6 molecules

#2: 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.: 2
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
#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.: 1
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
#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 / 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 , 2 types, 6 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN / Ubenimex


Mass: 308.373 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H24N2O4 / Comment: protease inhibitor*YM

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Details

Sequence detailsSEQUENCE CONFLICT IN UNP ENTRY Q9NZ08 AT THESE POSITIONS

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% PEG 8000, 0.1M Bicine pH 8.5, 1mM Glutathione, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 63768 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 5.1
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.765 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z5H

1z5h


Resolution: 2.95→38.106 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 3207 5.03 %
Rwork0.1988 --
obs0.202 63753 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.858 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.688 Å2-0 Å28.1721 Å2
2---10.0405 Å20 Å2
3----3.6474 Å2
Refinement stepCycle: LAST / Resolution: 2.95→38.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19902 0 261 0 20163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00520662
X-RAY DIFFRACTIONf_angle_d0.8527972
X-RAY DIFFRACTIONf_dihedral_angle_d22.05212355
X-RAY DIFFRACTIONf_chiral_restr0.0553159
X-RAY DIFFRACTIONf_plane_restr0.0033481
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A756X-RAY DIFFRACTIONPOSITIONAL
12B756X-RAY DIFFRACTIONPOSITIONAL1.839
13C756X-RAY DIFFRACTIONPOSITIONAL0.822
21A2607X-RAY DIFFRACTIONPOSITIONAL
22B2607X-RAY DIFFRACTIONPOSITIONAL0.384
23C2607X-RAY DIFFRACTIONPOSITIONAL0.392
31A701X-RAY DIFFRACTIONPOSITIONAL
32B701X-RAY DIFFRACTIONPOSITIONAL0.395
33C701X-RAY DIFFRACTIONPOSITIONAL0.618
41A763X-RAY DIFFRACTIONPOSITIONAL
42B763X-RAY DIFFRACTIONPOSITIONAL0.503
43C763X-RAY DIFFRACTIONPOSITIONAL0.533
51A1798X-RAY DIFFRACTIONPOSITIONAL
52B1798X-RAY DIFFRACTIONPOSITIONAL0.747
53C1798X-RAY DIFFRACTIONPOSITIONAL0.581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.05540.32943270.27635924X-RAY DIFFRACTION99
3.0554-3.17770.32213240.24966061X-RAY DIFFRACTION100
3.1777-3.32220.30983060.23346040X-RAY DIFFRACTION100
3.3222-3.49730.31113150.2156069X-RAY DIFFRACTION100
3.4973-3.71620.26753440.1916057X-RAY DIFFRACTION100
3.7162-4.00280.25433250.17516056X-RAY DIFFRACTION100
4.0028-4.40510.26042870.16346099X-RAY DIFFRACTION100
4.4051-5.04130.21573120.15646074X-RAY DIFFRACTION100
5.0413-6.34680.26363600.18916039X-RAY DIFFRACTION100
6.3468-38.10890.21983070.20266127X-RAY DIFFRACTION100
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)
10.739-0.5379-0.65550.80070.45050.8592-0.0445-0.0011-0.04920.0368-0.00230.14240.1656-0.0907-0.05260.0447-0.009-0.0550.09680.03170.0285-14.123652.6348-16.8763
20.74230.2174-0.16250.7999-0.13220.92220.07620.0507-0.0382-0.1727-0.0274-0.21530.05040.0416-0.01830.01940.04330.02240.0516-0.01760.049130.008984.7712-64.3253
30.79780.1939-0.31531.1735-0.18060.4903-0.0198-0.03450.0684-0.0976-0.02320.2106-0.0719-0.02210.0587-0.0027-0.026-0.08790.0285-0.03020.0904-16.5067124.9615-24.5819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 34:1000)
2X-RAY DIFFRACTION2(chain B and resid 34:1000)
3X-RAY DIFFRACTION3(chain C and resid 34:1000)

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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

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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

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