[English] 日本語
Yorodumi
- PDB-2wii: Complement C3b in complex with factor H domains 1-4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wii
TitleComplement C3b in complex with factor H domains 1-4
Components
  • COMPLEMENT C3 BETA CHAIN
  • COMPLEMENT C3B ALPHA' CHAIN
  • COMPLEMENT FACTOR H
KeywordsIMMUNE SYSTEM / SUSHI / SECRETED / POLYMORPHISM / GLYCOPROTEIN / COMPLEMENT SYSTEM / COMPLEMENT PATHWAY / IMMUNE RESPONSE / INNATE IMMUNITY / DISEASE MUTATION / INFLAMMATORY RESPONSE / COMPLEMENT ALTERNATE PATHWAY / CLEAVAGE ON PAIR OF BASIC RESIDUES / AGE-RELATED MACULAR DEGENERATION / REGULATOR OF COMPLEMENT ACTIVATION / ALTERNATIVE PATHWAY / ALTERNATIVE SPLICING / PHOSPHOPROTEIN / DISULFIDE BOND / THIOESTER BOND
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / vertebrate eye-specific patterning / complement component C3b binding ...regulation of complement activation, alternative pathway / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / vertebrate eye-specific patterning / complement component C3b binding / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of phagocytosis, engulfment / Activation of C3 and C5 / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / complement receptor mediated signaling pathway / positive regulation of D-glucose transmembrane transport / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / 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 / Regulation of Complement cascade / Peptide ligand-binding receptors / Post-translational protein phosphorylation / response to bacterium / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / heparin binding / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / receptor ligand activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / N-terminal domain of TfIIb ...Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / N-terminal domain of TfIIb / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement Module, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Complement Module; domain 1 / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Glycosyltransferase - #20 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / 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 / Other non-globular / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Single Sheet / Special / Ribbon / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Complement C3 / Complement factor H
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWu, J. / Janssen, B.J.C. / Gros, P.
CitationJournal: Nat. Immunol. / Year: 2009
Title: Structure of complement fragment C3b-factor H and implications for host protection by complement regulators.
Authors: Wu, J. / Wu, Y.Q. / Ricklin, D. / Janssen, B.J. / Lambris, J.D. / Gros, P.
History
DepositionMay 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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 2.1Dec 13, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COMPLEMENT C3 BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
C: COMPLEMENT FACTOR H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,59123
Polymers206,6913
Non-polymers2,90020
Water3,099172
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20690 Å2
ΔGint-52.49 kcal/mol
Surface area79820 Å2
MethodPISA
2
A: COMPLEMENT C3 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7836
Polymers71,3931
Non-polymers1,3895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: COMPLEMENT C3B ALPHA' CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,49215
Polymers104,0731
Non-polymers1,41814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: COMPLEMENT FACTOR H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3172
Polymers31,2251
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)223.489, 84.946, 128.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein COMPLEMENT C3 BETA CHAIN / COMPLEMENT C3 / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 1


Mass: 71393.320 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-667 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01024
#2: Protein COMPLEMENT C3B ALPHA' CHAIN / COMPLEMENT C3 / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 1


Mass: 104073.164 Da / Num. of mol.: 1 / Fragment: RESIDUES 749-1663 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01024
#3: Protein COMPLEMENT FACTOR H / H FACTOR 1


Mass: 31224.859 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSECTAG 2B-FH(1-4) / Cell line (production host): HEK293E / Production host: HOMO SAPIENS (human) / References: UniProt: P08603

-
Sugars , 2 types, 2 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D- ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-6)-[beta-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpb1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 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 , 3 types, 190 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsV44I IS A NATURALLY OCCURING VARIANT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.1
Details: 7.0% (W/V) PEG 3,350, 70 MM AMMONIUM ACETATE, PH 7.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.7→67 Å / Num. obs: 67945 / % possible obs: 99.7 % / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 52.69 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A74, PDB ENTRY 2I07, PDB ENTRY 1QUB, PDB ENTRY 1H03, PDB ENTRY 2RLP

2a74

2i07

1qub

1h03

2rlp


Resolution: 2.7→64.483 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: ML
Details: THE TOP PART OF THE FIRST CCP DOMAIN OF FACTOR H RESIDUES 1-65 ARE PARTIALLY DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2518 3436 5.1 %
Rwork0.2167 --
obs0.2184 67887 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.85 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 68.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.9085 Å2-0 Å2-0 Å2
2---19.1706 Å20 Å2
3----1.327 Å2
Refinement stepCycle: LAST / Resolution: 2.7→64.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14081 0 189 172 14442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214572
X-RAY DIFFRACTIONf_angle_d0.44619707
X-RAY DIFFRACTIONf_dihedral_angle_d14.3045432
X-RAY DIFFRACTIONf_chiral_restr0.032214
X-RAY DIFFRACTIONf_plane_restr0.0022531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7370.34961370.30382589X-RAY DIFFRACTION100
2.737-2.77610.32381360.29142510X-RAY DIFFRACTION100
2.7761-2.81750.29591350.28052547X-RAY DIFFRACTION100
2.8175-2.86160.31161450.2772568X-RAY DIFFRACTION100
2.8616-2.90850.31371470.27272530X-RAY DIFFRACTION100
2.9085-2.95860.30241310.26252554X-RAY DIFFRACTION100
2.9586-3.01240.27741320.2672563X-RAY DIFFRACTION100
3.0124-3.07040.33391510.25632545X-RAY DIFFRACTION100
3.0704-3.1330.31671250.26192575X-RAY DIFFRACTION100
3.133-3.20120.30431500.24532532X-RAY DIFFRACTION100
3.2012-3.27560.30591170.23462602X-RAY DIFFRACTION100
3.2756-3.35750.26491270.22622570X-RAY DIFFRACTION100
3.3575-3.44830.24831410.21642553X-RAY DIFFRACTION100
3.4483-3.54980.26491230.21162609X-RAY DIFFRACTION100
3.5498-3.66430.23861530.20822560X-RAY DIFFRACTION100
3.6643-3.79530.23151630.20052529X-RAY DIFFRACTION100
3.7953-3.94720.23411310.20012589X-RAY DIFFRACTION100
3.9472-4.12680.24181220.18252594X-RAY DIFFRACTION100
4.1268-4.34440.20771450.17552574X-RAY DIFFRACTION100
4.3444-4.61650.17881510.15012584X-RAY DIFFRACTION100
4.6165-4.97280.15171150.14362650X-RAY DIFFRACTION100
4.9728-5.4730.18611540.15662587X-RAY DIFFRACTION100
5.473-6.26440.21491380.1892619X-RAY DIFFRACTION99
6.2644-7.89020.18391330.20062591X-RAY DIFFRACTION96
7.8902-64.50130.23681340.20012727X-RAY DIFFRACTION97
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)
13.25080.3919-1.96263.30992.05851.741-0.277-0.036-0.8153-0.06630.07850.4260.1259-0.1381-0.00010.40890.05870.04850.32120.02220.610714.593-33.2102-53.8287
22.125-1.288-0.23762.35250.05322.1482-0.14860.033-0.04110.08890.1558-0.06240.28640.25140.00010.28150.105-0.01250.29780.02950.369323.8595-27.8128-18.2243
32.0330.01750.02991.6956-1.05521.7924-0.2178-0.0036-0.01040.2939-0.165-0.5434-0.12250.206-00.48340.0118-0.12150.42410.01580.71127.98817.0851-10.904
41.74130.73110.75942.26511.35021.1463-0.0250.06860.2438-0.29110.0748-0.1757-0.4362-0.155900.4070.05260.03540.40130.0430.630917.09425.299-43.9284
52.5009-0.51920.28912.8471-0.0781.41060.13940.3293-0.0137-0.6353-0.05810.1422-0.2063-0.24340.00010.49450.1161-0.05140.34480.00490.42176.1903-11.6258-54.6233
6-0.2213-0.3021-0.3033-0.2135-0.55880.0079-0.0447-0.1001-0.1291-0.10170.0725-0.0653-0.27950.381800.4764-0.00950.02130.461-0.00730.512520.0478-17.0631-40.926
71.707-0.7341-0.62081.42820.3622.1544-0.1363-0.0693-0.00730.16010.01590.3055-0.0298-0.4208-00.37520.07130.01870.43080.04180.38713.7584-19.8478-10.2625
80.30090.30670.00590.3782-0.25020.0448-0.2597-0.46410.12510.7344-0.00810.0239-0.2423-0.52070.00010.95550.2520.12870.7863-0.10350.479510.5001-18.989920.1962
91.31160.0734-0.44670.89040.03711.3399-0.4223-0.39960.24080.74270.3945-0.305-0.0764-0.0805-0.00010.89070.3168-0.17990.5862-0.0980.439921.0007-13.489817.8476
101.8787-0.43861.08112.1734-0.31682.91360.0717-0.0939-0.4320.08920.0912-0.16440.45620.26750.00010.48120.1774-0.01240.6193-0.06020.59146.9024-39.3064-10.5924
112.34360.35560.94353.2544-1.29382.7527-0.2805-0.32710.53470.75880.075-0.2447-0.4960.1633-0.00011.01120.1363-0.34980.5764-0.16890.918735.80823.180616.7844
121.0963-0.41250.10362.34560.09630.99420.0216-0.0098-0.04580.032-0.06440.05830.00540.0736-00.26750.01740.04080.45750.00460.270647.0566-49.9278-62.6505
133.05630.48530.34792.3463-0.37254.7934-0.0274-0.02740.0188-0.1122-0.23810.02560.11790.1804-0.00010.48530.03140.03330.5013-0.0140.428251.8488-33.917930.7669
140.13120.11590.12730.2330.31990.1278-0.4359-0.8583-0.19761.130.361.61210.1598-1.08530.00042.10930.62250.67591.52780.11850.9778-7.7402-22.438335.7521
150.94020.4053-0.09240.7713-0.12760.4912-0.259-0.2875-0.25440.69850.20760.47110.68810.2195-0.00020.89640.25880.17710.63590.07440.44987.4789-34.89685.5201
160.6012-0.6805-0.1190.47210.35620.9502-0.0919-0.1223-0.05620.43060.0349-0.32460.36360.475800.9898-0.00630.13730.5024-0.00930.61723.7624-51.3474-23.6237
171.34560.3799-0.77460.7891-0.03780.686-0.17680.2484-0.3253-0.12510.53320.7193-0.4071-0.51850.00010.78960.08880.02040.59660.00650.820921.9046-56.3396-56.8714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:104
2X-RAY DIFFRACTION2CHAIN A AND RESID 105:209
3X-RAY DIFFRACTION3CHAIN A AND RESID 210:328
4X-RAY DIFFRACTION4CHAIN A AND RESID 329:426
5X-RAY DIFFRACTION5CHAIN A AND RESID 427:534
6X-RAY DIFFRACTION6CHAIN A AND RESID 579:642
7X-RAY DIFFRACTION7CHAIN A AND RESID 535:578 OR CHAIN B AND RESID 746:806
8X-RAY DIFFRACTION8CHAIN B AND RESID 730:745
9X-RAY DIFFRACTION9CHAIN B AND RESID 807:911
10X-RAY DIFFRACTION10CHAIN B AND RESID 912:969 OR CHAIN B AND RESID 1269:1330
11X-RAY DIFFRACTION11CHAIN B AND RESID 1331:1474
12X-RAY DIFFRACTION12CHAIN B AND RESID 970:1268
13X-RAY DIFFRACTION13CHAIN B AND RESID 1475:1641
14X-RAY DIFFRACTION14CHAIN C AND RESID 1:64
15X-RAY DIFFRACTION15CHAIN C AND RESID 65:125
16X-RAY DIFFRACTION16CHAIN C AND RESID 126:189
17X-RAY DIFFRACTION17CHAIN C AND RESID 190:247

+
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