[English] 日本語
Yorodumi
- PDB-7noz: Structure of the nanobody stablized properdin bound alternative p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7noz
TitleStructure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP
Components
  • (Complement C3 ...) x 2
  • (Properdin) x 2
  • Complement factor B
  • hFPNb1 nanobody
KeywordsIMMUNE SYSTEM / protease / complement / cascade / proconvertase
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex ...cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / fatty acid metabolic process / positive regulation of immune response / positive regulation of receptor-mediated endocytosis / specific granule lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / tertiary granule lumen / secretory granule lumen / G alpha (i) signalling events / blood microparticle / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / serine-type endopeptidase activity / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / : / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Complement B/C2 ...TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / : / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Glycosyltransferase - #20 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / von Willebrand factor type A domain / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / Single Sheet / von Willebrand factor A-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Immunoglobulin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
alpha-D-mannopyranose / Complement factor B / Complement C3 / Properdin
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsLorenzen, J. / Pedersen, D.V. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
CitationJournal: Protein Sci. / Year: 2022
Title: Structure determination of an unstable macromolecular complex enabled by nanobody-peptide bridging.
Authors: Lorentzen, J. / Pedersen, D.V. / Gadeberg, T.A.F. / Andersen, G.R.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement C3 beta chain
B: Complement C3 alpha chain
C: Properdin
D: Properdin
F: Complement factor B
R: hFPNb1 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,06022
Polymers311,4986
Non-polymers5,56216
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.690, 179.460, 192.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Complement C3 ... , 2 types, 2 molecules AB

#1: Protein Complement C3 beta chain


Mass: 71393.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3 alpha chain


Mass: 103759.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024

-
Protein , 3 types, 3 molecules CDF

#3: Protein Properdin / Complement factor P


Mass: 17744.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P27918
#4: Protein Properdin / Complement factor P


Mass: 22958.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P27918
#5: Protein Complement factor B / C3/C5 convertase / Glycine-rich beta glycoprotein / GBG / PBF2 / Properdin factor B


Mass: 82084.609 Da / Num. of mol.: 1 / Mutation: D279G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFB, BF, BFD / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase

-
Antibody , 1 types, 1 molecules R

#6: Antibody hFPNb1 nanobody


Mass: 13557.077 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Sugars , 5 types, 15 molecules

#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Fucp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#10: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#11: 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.: 1
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

-
Non-polymers , 2 types, 3 molecules

#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Na-acetate pH 5.3, 0.1 M Mg-formate,7% PEG5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.9→48.59 Å / Num. obs: 47647 / % possible obs: 99.8 % / Redundancy: 39.7 % / Biso Wilson estimate: 196.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1949 / Net I/σ(I): 10.84
Reflection shellResolution: 3.9→4.039 Å / Redundancy: 43.8 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 4688 / CC1/2: 0.392 / % possible all: 99.91

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XWB

2xwb


Resolution: 3.9→48.59 Å / SU ML: 0.6713 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 34.0027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2654 1849 3.88 %
Rwork0.2488 45746 -
obs0.2494 47595 99.88 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 288.94 Å2
Refinement stepCycle: LAST / Resolution: 3.9→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21631 0 361 2 21994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003722465
X-RAY DIFFRACTIONf_angle_d0.712530457
X-RAY DIFFRACTIONf_chiral_restr0.07643426
X-RAY DIFFRACTIONf_plane_restr0.00783913
X-RAY DIFFRACTIONf_dihedral_angle_d14.11483204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.010.44651360.47033489X-RAY DIFFRACTION99.89
4.01-4.120.44681460.42893457X-RAY DIFFRACTION100
4.12-4.260.36311400.38063471X-RAY DIFFRACTION100
4.26-4.410.35711450.33843464X-RAY DIFFRACTION99.97
4.41-4.580.30421390.28833506X-RAY DIFFRACTION99.89
4.58-4.790.27691370.25623493X-RAY DIFFRACTION99.94
4.79-5.050.24171460.25163483X-RAY DIFFRACTION100
5.05-5.360.28711380.24653503X-RAY DIFFRACTION99.95
5.36-5.770.23841400.25163511X-RAY DIFFRACTION99.92
5.77-6.350.28171440.27553517X-RAY DIFFRACTION99.95
6.35-7.270.29381460.27933544X-RAY DIFFRACTION99.95
7.27-9.150.28491410.25543599X-RAY DIFFRACTION99.95
9.15-48.590.21381510.1873709X-RAY DIFFRACTION99.05
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)
10.200173168266-0.3412312444940.0636149201724-0.239576599669-0.7742768685152.24706788613-0.215074778143-0.0517508454411-0.1200700117390.2052699384260.0745067258043-0.07151518302010.1104328814650.1912782845791.85901439428E-51.95013083267-0.169553884584-0.03373216070991.73740652405-0.1451086441182.1569022848867.882315969733.6401225071-9.07888849736
20.523772863544-0.7208468161780.243356656810.9791381740950.4051851471350.513353764491-0.06954339247140.2298601110270.1467147422550.5413809428130.418583853774-0.606962840663-0.1808318325620.616391174487-4.75647730098E-51.984233783550.1490009996180.09483085798042.101757237760.06414115419261.9463052217445.60005031152.8896864301310.15419473
30.5431956798070.757013800507-0.05583196692051.21810986904-0.4504947532230.309268333298-0.44250051045-0.263371904151-0.3818701588260.4868628657970.495883375024-0.5802072744460.152016688743-0.823255238604-2.7242408991E-53.09779679830.8891699522170.2359492288763.14553524558-0.1053447368681.9102273243148.412324657917.155332459761.1282099272
42.85191118328-0.553369881947-0.1132016945881.349598475690.853090325923.14633973301-1.12649227983-0.343128115549-0.603425728836-0.5890715727020.6040499630540.7203052598292.078374902310.506039952939-0.8997260503922.2586943632-1.35880698938-0.548166955514-0.210703234164-0.07180087927721.9373103281636.1965451824-3.57749863175-43.0257810814
51.085605571471.00061464907-0.4111827680560.946914854856-0.07957329875611.37529355993-0.122870229847-0.6704012432380.07919397874070.228525142448-0.323117711362-0.3924513567280.674657378050.506125429329.46598821311E-52.452173460640.549391582589-0.02127954884932.5994138650.08277337740991.8822369338284.183181808721.660311242436.7617764804
61.42264502313-2.79026325866-1.026894495985.356689754441.880567593480.652888856851-2.487738837483.95880262857-0.9105323151782.96082996271-0.381743536962.12858777787-0.7884423835992.30735077089-1.739538965266.66843234202-0.130216121927-0.7986450529696.5322376811.102863833193.601018162011.3861154808513.267545245157.631538568
70.5843353637360.2096430779710.006922787283170.08186428573720.00983182198231-0.0002327766064220.708982116596-1.27474266805-1.442828002310.6249416213210.7245180364750.02029298348771.10715867738-0.1882173019230.01733703885046.024092369413.12629392124-0.02827441379747.691409628290.4494747224613.3139412314672.6592513309-14.217348316126.681169765
81.365205799030.0423625228553-0.340239968402-0.02108572436550.1898758136210.370970551549-0.421543335372-0.5013864048420.149495820051-0.06813413403430.3524788904360.5930095739870.4628716284720.2313806466832.74035344496E-53.25734768460.7066608118730.3075813886743.61943638481-0.02293834503342.4313165100629.807254623727.413204523399.207569196
90.0428053296032-0.0933655678716-0.06298580858270.1613906303160.21832813330.2579900762530.919030214412-1.22548970534-1.53997947582-1.56423193108-1.16720605005-0.92494808135-0.323964511348-0.890564909064-5.36072807309E-53.873625064260.6297671758420.6252279494714.054122720010.2303833100633.2593533979660.3158030067.88450566042111.967998846
100.1323573622670.03087632628680.2017496221150.01138521472850.0681853685570.3525378267921.181623344960.351662967772-0.0554977257126-0.05260582235180.701503370101-0.2043938541770.04599556079841.269834248860.0013825996084.372041906660.368222242782-0.6639941303052.387166705860.00372443192193.1736843510341.770436011147.382986655953.2919523605
111.74726411308-0.490426067954-0.243035942510.5041856289290.4893929490970.764824623177-0.233704654617-0.08805810784030.0003075492844130.2138339705630.0948867526450.646315810297-0.290066522806-0.193232113187-3.70325532262E-52.636999078050.2325646030070.4251122208512.306174952390.05293571879063.2403177818341.176064167136.27056861922.7109739526
123.15836522893-0.02008956039980.2652966634511.92691738330.6355050916543.493285677-0.7217101022470.2123729143930.01069094544570.6729975169250.247192259906-0.00533577011821-0.0137467692058-0.542443876792-8.83976721228E-62.088337875620.5175660279660.3191381611952.370211507020.1694772499742.1441376107818.979604211826.305714842641.7535242517
131.21000188086-0.1254828915140.1213793938251.766987435290.5439756580872.30675255485-0.0106928721726-0.31783395881-0.0303447802713-0.2827066811010.01348904721530.3076996693110.1816023981220.115394871272-7.89963097753E-52.024131964050.174261710592-0.09902785325522.329577032740.1109829964213.0036357808816.153322344823.5964656047-0.169481132077
140.1262777486420.22957508724-0.02884833299590.2463940512740.0920322850930.107256119242-0.9226890227570.37203161716-0.9326750276560.730382249911.15802265426-0.348960954085-0.963460764561-2.199674967550.0003949419621393.840558233851.378856525170.5378451144286.102418698721.249468091514.6570392816753.95414183-18.5762314095105.830121108
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label seq-ID
11(chain A or (chain B and resid 751:932))A - BA - E23 - 9321 - 181
22(chain B and (resid 933:1356 or resid 1664:1666) and not (resid 989:1299))BE - H933 - 1666182
33(chain B and resid 1500:1663 )BE1500 - 1663743 - 906
44(chain B and resid 989:1299)BE989 - 1299238 - 548
55(chain B and resid 1357:1499)BE1357 - 1499606 - 742
66(chain C and (resid 134:190 or resid 1029:1031 or resid 1023:1024))CI - P134 - 1031107
77(chain D and (resid 255:264 or resid 281:301 or resid 1096:1097))DQ255 - 3011 - 47
88((chain D and not (resid 255:310 or resid 1036:1037 or resid 1096:1097)) or (chain C and not (resid 28:75 or resid 134:190 or resid 1029:1031 or resid 1023:1024)))C - KI - L76 - 110149
99((chain D and (resid 265:280 or resid 302:310 or resid 1036:1037)) or (chain C and resid 28:75))C - DI - S28 - 10371
1010(chain F and resid 35:101)FE35 - 1011 - 67
1111(chain F and (resid 102:224 or resid 767:768 or resid 1025:1026 or resid 1032:1034))F - ME - N102 - 103368
1212(chain F and (resid 225:248 or resid 260:476 or resid 1027:1030 )) or (chain E)FV - E1 - 476423
1313(chain F and resid 477:766)FE477 - 765424 - 712
1414(chain R)RF2 - 1251 - 124

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more