[English] 日本語
Yorodumi
- PDB-6ruv: Structure of the SCIN stabilized C3bBb convertase bound to Proper... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ruv
TitleStructure of the SCIN stabilized C3bBb convertase bound to Properdin and a the non-inhibitory nanobody hFPNb1
Components
  • (Complement C3) x 2
  • (Properdin) x 2
  • Complement factor B
  • Inhibitor
  • Nanobody hFPNb1
KeywordsIMMUNE SYSTEM / innate immunity / complement / proteolytic enzyme / regulator / nanobody
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 / positive regulation of activation of membrane attack complex / complement binding ...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 / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / Activation of C3 and C5 / positive regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / positive regulation of D-glucose transmembrane transport / complement-dependent cytotoxicity / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / neuron remodeling / B cell activation / amyloid-beta clearance / 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 / fatty acid metabolic process / response to bacterium / Post-translational protein phosphorylation / 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 angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / tertiary granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / positive regulation of protein phosphorylation / defense response to bacterium / immune response / inflammatory response / receptor ligand activity / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / 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
Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / : / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / Complement factor B / Complement B/C2 / Complement C3-like, NTR domain ...Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / : / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / Complement factor B / Complement B/C2 / 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 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / 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) / Heat shock protein 70kD, C-terminal domain superfamily / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / 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 / Peptidase S1, PA clan
Similarity search - Domain/homology
alpha-D-mannopyranose / Staphylococcal complement inhibitor / Complement factor B / Complement C3 / Properdin / Staphylococcal complement inhibitor
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.15 Å
AuthorsPedersen, D.V. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
Citation
Journal: Front Immunol / Year: 2019
Title: Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.
Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / ...Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / Laursen, N.S. / Fremeaux-Bacchi, V. / Andersen, G.R.
#1: Journal: Febs Lett. / Year: 2019
Title: Crystal structure of peptide-bound neprilysin reveals key binding interactions.
Authors: Moss, S. / Subramanian, V. / Acharya, K.R.
History
DepositionMay 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_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.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: Nanobody hFPNb1
S: Nanobody hFPNb1
U: Properdin
V: Properdin
X: Properdin
Y: Properdin
A: Complement C3
B: Complement C3
G: Complement C3
H: Complement C3
J: Complement factor B
L: Complement factor B
N: Inhibitor
Q: Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)610,52652
Polymers600,52614
Non-polymers10,00038
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58820 Å2
ΔGint-109 kcal/mol
Surface area249760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.990, 354.030, 367.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 6 types, 12 molecules UXVYAGBHJLNQ

#2: Protein Properdin / Complement factor P


Mass: 18636.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TSR2 is not modelled and therefore missing residues
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / Variant (production host): HEK293F / References: UniProt: P27918
#3: Protein Properdin / Complement factor P


Mass: 24724.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Properdin TSR4-TSR5-TSR6 and a few additional residues from vector
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / References: UniProt: P27918
#4: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 71393.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: beta-chain / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#5: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 104073.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: alpha-prime chain / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#6: Protein Complement factor B / C3/C5 convertase / Glycine-rich beta glycoprotein / GBG / PBF2 / Properdin factor B


Mass: 57042.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Bb fragment / Source: (gene. exp.) Homo sapiens (human) / Gene: CFB, BF, BFD / Production host: Homo sapiens (human) / Variant (production host): HEK293F
References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase
#7: Protein Inhibitor / Involved in expression of fibrinogen binding protein / phage associated / Staphylococcal complement inhibitor


Mass: 9876.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: scn_3, scn, scn_2, scn_4, BN1321_320035, CV021_13080, D1G05_09530, D1G09_13565, D1G21_11725, EP54_10460, EQ90_13920, ERS072840_02186, NCTC10654_02112, NCTC10702_03129, NCTC13196_02025, ...Gene: scn_3, scn, scn_2, scn_4, BN1321_320035, CV021_13080, D1G05_09530, D1G09_13565, D1G21_11725, EP54_10460, EQ90_13920, ERS072840_02186, NCTC10654_02112, NCTC10702_03129, NCTC13196_02025, NCTC13196_03045, NCTC6133_02657, NCTC7878_02651
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2DUF0, UniProt: Q931M7*PLUS

-
Antibody / Non-polymers , 2 types, 4 molecules RS

#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#1: Antibody Nanobody hFPNb1


Mass: 14517.155 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Sugars , 4 types, 36 molecules

#8: Polysaccharide
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-Glycam 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
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#9: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#10: 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.: 8
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
#11: Sugar...
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 21
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.72 Å3/Da / Density % sol: 81.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 100 mM NaCl, 5 % (w/v) PEG4000, 10 mM MgCl2, 100 mM Sodium Cacodylate trihydrate pH 5.8.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 6.15→50 Å / Num. obs: 38393 / % possible obs: 99.6 % / Redundancy: 13 % / Net I/σ(I): 12.2
Reflection shellResolution: 6.15→6.31 Å / Num. unique obs: 2738

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WIN

2win


Resolution: 6.15→49.819 Å / SU ML: 1.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.76
RfactorNum. reflection% reflection
Rfree0.2707 1990 5.19 %
Rwork0.2422 --
obs0.2437 38338 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 6.15→49.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41278 0 638 0 41916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542911
X-RAY DIFFRACTIONf_angle_d0.95158292
X-RAY DIFFRACTIONf_dihedral_angle_d16.54826312
X-RAY DIFFRACTIONf_chiral_restr0.0576549
X-RAY DIFFRACTIONf_plane_restr0.0087437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.1501-6.30360.46371480.43722485X-RAY DIFFRACTION98
6.3036-6.47370.42281330.41092581X-RAY DIFFRACTION100
6.4737-6.66380.40381410.39172551X-RAY DIFFRACTION100
6.6638-6.87840.39591490.3682561X-RAY DIFFRACTION100
6.8784-7.12350.3411300.34252553X-RAY DIFFRACTION100
7.1235-7.40790.34081430.31892595X-RAY DIFFRACTION100
7.4079-7.74380.3431420.30062598X-RAY DIFFRACTION100
7.7438-8.15040.29091400.27662571X-RAY DIFFRACTION100
8.1504-8.65860.30911400.24662587X-RAY DIFFRACTION100
8.6586-9.32310.22571450.22762603X-RAY DIFFRACTION100
9.3231-10.2540.22831430.20042628X-RAY DIFFRACTION100
10.254-11.72080.22581390.19082623X-RAY DIFFRACTION99
11.7208-14.70380.23191450.20342648X-RAY DIFFRACTION99
14.7038-49.82030.26961520.23252764X-RAY DIFFRACTION99
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)
11.17671.16560.12983.43390.65350.673-0.2402-0.14780.17930.37080.3754-0.2265-0.37230.3528-0.08164.4023-0.0071-0.08934.3225-0.00384.2883-4.2255-49.69489.947
24.151-2.44090.60623.066-0.27610.885-0.04960.0076-0.1259-0.91690.3136-0.0243-0.1801-0.1289-0.18484.4482-0.29860.01244.3328-0.03943.9286-14.7996-53.0208-34.8429
36.6091.02360.96629.5688-2.52316.3367-1.087-2.18520.07333.36330.7585-0.9123-4.77561.44250.31684.63370.0554-0.49414.1732-0.17393.1272-9.0606-47.531148.9092
45.3996-2.171-0.36715.96220.87852.01580.74531.5867-0.4102-1.4692-0.7674-1.1403-1.4868-1.90550.15097.0602-0.45010.30795.24310.12054.6213-14.1921-46.5243-73.6161
57.00190.16241.76848.02334.17392.7509-0.0469-0.1885-0.98682.55150.2580.56090.1625-0.6092-0.13834.88140.77910.29615.17690.37845.00833.7483-99.568351.2353
63.7356-5.2342-4.82350.03650.23215.7570.55610.38330.569-1.78880.33160.0621-0.42671.1232-0.65195.5344-0.19830.58233.8992-0.17984.393314.5242-91.6122-78.5732
74.42642.40852.23185.44232.90223.2532-0.3488-0.62460.79030.27350.0950.7127-0.524-0.62820.35323.76330.67110.46224.4260.23794.2098-55.4654-26.237216.9681
82.4499-1.59230.44592.7145-1.23482.6509-0.15050.35630.2753-0.49640.0985-1.1081-0.910.72010.01124.7737-0.41020.55044.36110.36145.34772.57211.2725-39.9546
91.84571.74380.77815.93914.43597.94890.67550.57081.0167-3.53530.20560.5682-2.5584-1.2084-0.5264.6769-0.0326-0.40194.86810.94255.7012-10.3685-7.9041-18.3933
105.7116-3.88431.64335.9615-3.13368.2370.1546-2.87151.60162.66890.6769-4.4059-1.2647-0.5107-0.30094.65310.1071-0.35193.9391-0.63325.0484-40.3683-21.6399-4.6265
111.78180.2768-0.09491.4786-0.29451.1133-2.0234-0.9518-5.61861.49331.7469-1.67321.24761.82010.68857.96240.88570.73227.9576-1.90589.7127-47.995450.371562.7407
121.0197-0.2059-0.83850.4193-0.46991.2237-2.83352.4173-0.4527-0.94262.10983.23295.2114-4.99190.175911.68520.0478-4.23468.1976-2.0315.4115-70.033844.764453.6126
130.79180.1654-0.5597-0.1970.36610.40390.89840.58190.73390.39180.87142.40531.6315-1.0255-0.89027.89321.3479-0.58488.3206-4.654312.058-33.035652.76181.265
145.7062-1.3391-2.70783.18551.36475.6284-3.41232.31731.08450.82154.03922.4469-2.58031.9026-1.66015.1691-0.22060.06795.06730.08826.3907-54.758520.356539.1745
151.11211.55530.95361.4257-0.37421.2256-0.4754-0.26440.4858-1.6217-1.63583.37550.1299-1.05891.84726.23040.71580.17057.5584-1.21068.4644-76.666229.568140.1967
161.53160.7977-2.29990.4238-1.20373.4522-0.5775-1.348-0.4149-0.0797-0.31620.06360.8174-1.18060.73478.7019-2.5149-4.02897.1276-0.256511.8243-67.27912.511652.7457
171.1985-1.0321-0.8333.34020.6482.23150.4269-0.44341.526-5.00391.1541-2.1137-0.6249-3.058-0.53397.9199-0.12741.05625.992.00995.8652-60.868448.7983-81.4962
181.7645-1.0541.32614.20980.24271.23033.9069-2.95380.43821.165-4.14250.53760.84211.22581.19076.9827-1.42420.69746.52850.79754.4406-42.718261.8554-71.1013
196.2968-0.31380.25550.6453-0.51071.5573-1.69821.94011.01181.0248-2.1659-3.2952-4.84960.42162.2696.89670.15181.02824.79950.86595.895-23.3673105.933-92.1196
206.40294.6509-0.10189.94891.3122.47680.7744-0.5417-1.26450.0662-0.8361-1.132-4.08441.45650.84587.2690.09770.76364.40810.43025.749-73.221142.0993-99.539
216.0094-0.63253.95774.6455-0.63181.68552.7711-3.58081.930.3143-1.7330.00711.9798-2.5145-1.87354.2221-1.06620.10694.9450.21233.8094-33.389532.997-59.264
221.08421.567-1.46893.6127-1.70225.2552-1.02440.60321.1384-0.58421.40420.2704-3.26321.132-0.74126.9081-0.31270.51334.88180.17495.1315-26.892155.8095-57.9164
234.63636.3281.35168.60181.81746.2358-0.16161.14160.3683-0.4776-0.3240.3262-0.12850.91450.13374.9419-3.6003-0.89085.38-3.541710.3265-19.819839.4931-71.0767
245.620.5924-0.03633.70451.92560.5055-1.038-3.1017-0.37361.7030.4181.5491-2.7559-2.35120.05348.37990.80390.62698.42170.09156.8748-54.913932.675-107.6228
253.0399-0.45690.21020.6903-0.79070.2534-3.0039-1.99860.3386-3.06771.6047-0.2403-0.77620.51680.381610.80392.2605-2.268613.5674-6.846811.3842-37.109331.837887.7084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain A) or (chain B and resseq 729:910) or (chain B and resseq 1335:1479))
2X-RAY DIFFRACTION2((chain G) or (chain H and resseq 729:910) or (chain H and resseq 1335:1479))
3X-RAY DIFFRACTION3(chain B and resseq 911:966) or (chain B and resseq 1268:1334 ) or (chain B and resseq 2001:2003))
4X-RAY DIFFRACTION4(chain H and resseq 911:966) or (chain H and resseq 1268:1334 ) or (chain H and resseq 2001:2003))
5X-RAY DIFFRACTION5(chain B and resseq 967:1267)
6X-RAY DIFFRACTION6(chain H and resseq 967:1267)
7X-RAY DIFFRACTION7(chain B and resseq 1480:1641 ) or (chain L) )
8X-RAY DIFFRACTION8(chain H and resseq 1480:1641 ) or (chain J) )
9X-RAY DIFFRACTION9chain Q
10X-RAY DIFFRACTION10chain N
11X-RAY DIFFRACTION11chain U and resid 28:75
12X-RAY DIFFRACTION12chain U and ((resid 76:133) or (resid 1025) or (resid 1026) or (resid 1027:1028))
13X-RAY DIFFRACTION13chain V and ((resid 255:312) or (resid 1097) or (resid 1096) or (resid 1036:1037))
14X-RAY DIFFRACTION14chain V and ((resid 313:378) or (resid 1038) or (resid 1039) )
15X-RAY DIFFRACTION15chain V and ((resid 379:480) or (resid 1040) or (resid 1046) or (resid 1048))
16X-RAY DIFFRACTION16chain V and resid 1042:1044
17X-RAY DIFFRACTION17chain X and resid 28:75
18X-RAY DIFFRACTION18chain X and ((resid 76:133) or (resid 1025) or (resid 1026) or (resid 1027:1028))
19X-RAY DIFFRACTION19chain X and ((resid 134:191) or (resid 1029) or (resid 1030) or (resid 1031) or (resid 1023:1024))
20X-RAY DIFFRACTION20chain Y and ((resid 255:312) or (resid 1097) or (resid 1096) or (resid 1036:1037))
21X-RAY DIFFRACTION21chain Y and ((resid 313:378) or (resid 1038) or (resid 1039) )
22X-RAY DIFFRACTION22chain Y and ((resid 379:480) or (resid 1040) or (resid 1046) or (resid 1048))
23X-RAY DIFFRACTION23chain Y and resid 1042:1044
24X-RAY DIFFRACTION24chain R
25X-RAY DIFFRACTION25chain S

+
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