[English] 日本語
Yorodumi
- PDB-3ohx: Molecular Basis for Complement Recognition and Inhibition Determi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ohx
TitleMolecular Basis for Complement Recognition and Inhibition Determined by Crystallographic Studies of the Staphylococcal Complement Inhibitor (SCIN) Bound to C3c and C3b
Components
  • (Complement C3Complement component 3) x 3
  • Staphylococcal complement inhibitor
KeywordsIMMUNE SYSTEM / Complement Component C3 / Complement alternate pathway / Complement Pathway / Convertase / Immune evasion / Innate Immunity / Secreted Virulence Factor
Function / homology
Function and homology information


oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / 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 / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / 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 / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 ...Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / N-terminal domain of TfIIb / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / 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 / Heat shock protein 70kD, C-terminal domain superfamily / Other non-globular / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Single Sheet / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Complement C3 / Staphylococcal complement inhibitor
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.503 Å
AuthorsGeisbrecht, B.V. / Garcia, B.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Molecular Basis for Complement Recognition and Inhibition Determined by Crystallographic Studies of the Staphylococcal Complement Inhibitor (SCIN) Bound to C3c and C3b.
Authors: Garcia, B.L. / Ramyar, K.X. / Tzekou, A. / Ricklin, D. / McWhorter, W.J. / Lambris, J.D. / Geisbrecht, B.V.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionSep 1, 2010ID: 3NSA
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 24, 2013Group: Refinement description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement C3
B: Complement C3
C: Complement C3
E: Complement C3
M: Staphylococcal complement inhibitor
P: Staphylococcal complement inhibitor
F: Complement C3
D: Complement C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,67510
Polymers289,2338
Non-polymers4422
Water0
1
A: Complement C3
B: Complement C3
C: Complement C3
M: Staphylococcal complement inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8385
Polymers144,6164
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Complement C3
P: Staphylococcal complement inhibitor
F: Complement C3
D: Complement C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8385
Polymers144,6164
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.159, 231.497, 68.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Complement C3 / Complement component 3


Mass: 71393.320 Da / Num. of mol.: 2 / Fragment: Complement C3 beta chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3 / Complement component 3


Mass: 23621.244 Da / Num. of mol.: 2 / Fragment: Complement C3 alpha' chain fragment 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#3: Protein Complement C3 / Complement component 3


Mass: 39537.418 Da / Num. of mol.: 2 / Fragment: Complement C3 alpha' chain fragment 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#4: Protein Staphylococcal complement inhibitor / SCIN


Mass: 10064.370 Da / Num. of mol.: 2 / Fragment: Staphylococcal Complement Inhibitor-A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV1942, scn / Plasmid: PT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q931M7
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5mg/ml protein, 0.1M HEPES, 10% PEG6000, 5% 2-Methyl-2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2009 / Details: Mirror
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 10.55 / Number: 329081 / Rmerge(I) obs: 0.121 / Χ2: 1.01 / D res high: 3.5 Å / D res low: 50 Å / Num. obs: 44393 / % possible obs: 93.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.535099.910.0551.08912.9
5.987.5399.610.1170.98311.7
5.235.9896.910.1460.9749.6
4.755.2395.310.1411.0758.1
4.414.7594.410.1521.0646.8
4.154.4194.310.1851.0695.7
3.944.1591.710.2530.9335
3.773.9489.110.3240.8884.5
3.633.7786.910.3860.8424
3.53.6385.110.4660.8693.7
ReflectionResolution: 3.5→50 Å / Num. all: 44393 / Num. obs: 44393 / % possible obs: 93.4 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 / Redundancy: 7.4 % / Rmerge(I) obs: 0.121 / Χ2: 1.01 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.5-3.633.70.46639990.869185.1
3.63-3.7740.38640430.842186.9
3.77-3.944.50.32441610.888189.1
3.94-4.1550.25342990.933191.7
4.15-4.415.70.18544311.069194.3
4.41-4.756.80.15244291.064194.4
4.75-5.238.10.14145361.075195.3
5.23-5.989.60.14646250.974196.9
5.98-7.5311.70.11748180.983199.6
7.53-5012.90.05550521.089199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.64 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å46.96 Å
Translation3.5 Å46.96 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
RESOLVEphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.503→46.275 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.76 / SU ML: 0.47 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2938 2014 4.55 %Random
Rwork0.2738 ---
obs0.2747 44269 93.09 %-
all-44338 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.826 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso max: 246.51 Å2 / Biso mean: 69.1916 Å2 / Biso min: 12.33 Å2
Baniso -1Baniso -2Baniso -3
1-5.9083 Å2-0 Å20 Å2
2---13.7816 Å20 Å2
3---22.3679 Å2
Refinement stepCycle: LAST / Resolution: 3.503→46.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19091 0 28 0 19119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119508
X-RAY DIFFRACTIONf_angle_d1.31826407
X-RAY DIFFRACTIONf_chiral_restr0.0783011
X-RAY DIFFRACTIONf_plane_restr0.0073393
X-RAY DIFFRACTIONf_dihedral_angle_d20.3637260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.503-3.62860.35641790.33423730390984
3.6286-3.77380.32591920.32953869406187
3.7738-3.94540.29451880.31443967415589
3.9454-4.15330.33181910.30764115430691
4.1533-4.41340.30552010.27114242444394
4.4134-4.75380.27462110.24814229444094
4.7538-5.23160.24292010.23314342454395
5.2316-5.98730.31472070.24984405461297
5.9873-7.5380.27562180.25846084826100
7.538-46.2790.2552260.24184748497499
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)
10.2186-0.4192-0.08460.23670.38930.5250.12890.12150.13880.8610.25-0.3885-0.0936-0.463700.4027-0.1226-0.22870.38530.02710.4952-29.5919-56.370156.4155
20.45890.22730.10990.0222-0.2760.62150.05190.01880.1567-0.08840.0953-0.07370.099-0.028300.28510.0042-0.04320.1918-0.0173-0.0334-29.455-21.72527.8025
30.49720.2493-0.26020.0727-0.30460.3818-0.12280.06240.1795-0.03260.3122-0.47640.2778-0.267300.6525-0.0595-0.09180.4919-0.01420.3104-45.5454-50.571419.474
40.5659-0.00230.08240.37560.05760.56980.0770.0085-0.0308-0.0832-0.09580.30220.0792-0.0167-00.3298-0.0214-0.04820.2941-0.0540.4791-47.5963-56.107142.1339
5-0.27450.28470.32610.3576-0.6197-1.74670.2683-0.38730.28220.02760.18180.0812-0.33050.377500.20170.1003-0.12840.21640.11730.0097-39.0263-28.167242.5059
60.02590.02810.04370.0221-0.0516-0.00330.16910.0233-0.0873-0.2251-0.30980.0799-0.7885-0.2078-00.6882-0.09790.10210.39750.0630.469-25.1557-53.272838.0294
70.4899-0.10320.15410.25530.2055-0.04640.0016-0.30190.4570.05590.12350.33560.01210.0333-00.3577-0.02160.07150.1478-0.04260.0934-40.8368-5.093145.6067
80.09060.08680.01340.0344-0.2160.2661-0.24190.1386-0.2725-0.0580.2624-0.0079-0.0327-0.077300.2557-0.00520.05550.2054-0.04590.4359-32.856711.972729.2754
90.02810.2245-0.02330.1894-0.39470.0912-0.0388-0.04150.29030.0070.05440.0136-0.0317-0.01200.31890.04510.04570.2551-0.08360.4494-29.669216.436134.1339
100.98030.3724-0.09480.70650.06070.7742-0.03270.29320.4328-0.10780.1129-0.0745-0.15460.120400.3229-0.04320.10570.28210.08970.5013-23.677814.025513.671
110.70380.3110.17120.7339-0.17360.18960.0423-0.11470.25610.3634-0.11660.1771-0.06260.095500.5946-0.11880.09330.4386-0.13890.9321-6.94739.918338.3663
12-0.0398-0.10240.0958-0.0266-0.1086-0.015-0.05151.46120.6761-0.6561-0.9114-0.1630.57090.63020-0.1904-0.95810.2063-0.7097-0.38641.6985-10.284356.296741.8388
130.15680.09970.09680.1331-0.15720.4059-0.09630.48150.47070.14940.1156-0.14510.4260.0457-00.8045-0.1593-0.25510.74410.02750.6723-83.7983-57.126410.5457
140.5564-0.29430.84630.22090.19680.2890.11810.07270.06190.07440.08070.21040.0564-0.1588-00.1976-0.10740.02010.33570.18850.2387-92.7755-21.974721.0476
150.7620.3305-0.15190.23330.34280.14440.1084-0.19080.2759-0.120.0929-0.06660.12910.035700.3595-0.0162-0.05960.40470.05360.1872-79.3668-22.823751.6183
160.2881-0.1784-0.1657-0.00930.29910.22750.06720.0591-0.13650.35660.4591-0.3220.49340.551500.83750.0102-0.10520.64310.01530.4712-67.9655-50.873747.4238
170.22380.096-0.06550.3279-0.19530.53660.2178-0.14220.1353-0.21150.0288-0.20720.2472-0.0583-00.2922-0.0774-0.15920.26490.0480.3058-67.6267-42.30924.0362
180.1693-0.15540.0788-0.0992-0.0737-0.25541.78391.09851.20230.96510.44110.8181-2.317-1.61760-1.7068-0.7195-1.79720.1721-0.3155-1.0494-82.2646-49.405927.5219
190.76220.27690.39590.0790.28690.34330.00230.16180.2455-0.14070.07280.14740.06750.035100.2438-0.04590.05030.22120.15710.259-73.9222-5.532721.3039
200.0375-0.1081-0.15750.00830.33030.4240.46780.1618-0.03470.0726-0.1054-0.12210.1652-0.0557-00.1515-0.04120.11420.32730.20280.7361-85.80988.824237.736
210.1113-0.2750.15350.1063-0.06220.2385-0.15310.21270.15850.15160.25960.0218-0.1231-0.141300.22870.0330.06360.40680.15770.6233-84.152715.995933.311
220.5492-0.41290.440.449-0.04861.30810.1683-0.2915-0.1070.07310.05670.1763-0.58960.527600.4775-0.13470.26850.4727-0.0450.5961-90.518612.749254.9496
23-0.08740.0766-0.0628-0.01320.0441-0.01830.16180.0869-0.52650.19390.16520.2353-0.4431-0.0532-00.72070.02520.18870.63910.24590.8897-103.911624.84731.9399
240.7742-0.12210.35930.71470.10450.4450.3559-0.1296-0.0838-0.5026-0.21560.4398-0.05350.009600.0076-0.03540.07430.1864-0.06860.6397-108.990838.802428.5049
250.08630.04460.0601-0.0680.0963-0.03980.1239-0.22850.19160.057-0.4640.25280.12150.0327-00.1709-0.0858-0.06440.46520.19230.8434-105.768654.314221.8708
260.0011-0.01240.0214-0.0475-0.0591-0.03970.0956-0.00540.01390.2795-0.12960.16220.13660.1459-00.5817-0.11720.23170.4726-0.17030.8983-65.223626.047450.3181
270.1348-0.05170.07440.10570.1117-0.07510.0767-0.04930.59160.1846-0.3019-0.03310.05890.220200.4901-0.01440.19460.452-0.09490.6378-51.085516.760148.4337
280.00350.0067-0.00530.00310.01140.0070.0540.0599-0.13790.1036-0.12640.13630.1199-0.2801-00.7032-0.0752-0.03920.853-0.12130.8454-47.95413.819162.3835
290.03020.01850.0880.0389-0.11-0.07480.08330.18620.5087-0.165-0.0620.2947-0.4785-0.0344-00.4999-0.00660.16380.45230.1570.7903-50.360526.202716.5562
300.0998-0.0703-0.01150.123-0.1230.18690.01650.04510.5123-0.1020.15180.25930.0942-0.0328-00.3934-0.01640.05520.52710.19550.4532-64.251516.55518.4657
31-0.0005-0.0074-0.01520.00450.00090.01350.04210.0012-0.1946-0.07280.1342-0.13930.10470.300700.9789-0.05160.05110.95830.16530.5022-67.05173.51124.5391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:105)A1 - 105
2X-RAY DIFFRACTION2(CHAIN A AND RESID 106:362)A106 - 362
3X-RAY DIFFRACTION3(CHAIN A AND RESID 363:433)A363 - 433
4X-RAY DIFFRACTION4(CHAIN A AND RESID 434:533)A434 - 533
5X-RAY DIFFRACTION5(CHAIN A AND RESID 534:629)A534 - 629
6X-RAY DIFFRACTION6(CHAIN A AND RESID 630:645)A630 - 645
7X-RAY DIFFRACTION7(CHAIN B AND RESID 729:812)B729 - 812
8X-RAY DIFFRACTION8(CHAIN B AND RESID 813:843)B813 - 843
9X-RAY DIFFRACTION9(CHAIN B AND RESID 844:912)B844 - 912
10X-RAY DIFFRACTION10(CHAIN C AND RESID 1336:1493)C1336 - 1493
11X-RAY DIFFRACTION11(CHAIN C AND RESID 1494:1609)C1494 - 1609
12X-RAY DIFFRACTION12(CHAIN C AND RESID 1610:1641)C1610 - 1641
13X-RAY DIFFRACTION13(CHAIN D AND RESID 1:105)D1 - 105
14X-RAY DIFFRACTION14(CHAIN D AND RESID 106:208)D106 - 208
15X-RAY DIFFRACTION15(CHAIN D AND RESID 209:362)D209 - 362
16X-RAY DIFFRACTION16(CHAIN D AND RESID 363:433)D363 - 433
17X-RAY DIFFRACTION17(CHAIN D AND RESID 434:586)D434 - 586
18X-RAY DIFFRACTION18(CHAIN D AND RESID 587:645)D587 - 645
19X-RAY DIFFRACTION19(CHAIN E AND RESID 729:812)E729 - 812
20X-RAY DIFFRACTION20(CHAIN E AND RESID 813:835)E813 - 835
21X-RAY DIFFRACTION21(CHAIN E AND RESID 836:912)E836 - 912
22X-RAY DIFFRACTION22(CHAIN F AND RESID 1336:1481)F1336 - 1481
23X-RAY DIFFRACTION23(CHAIN F AND RESID 1482:1498)F1482 - 1498
24X-RAY DIFFRACTION24(CHAIN F AND RESID 1503:1609)F1503 - 1609
25X-RAY DIFFRACTION25(CHAIN F AND RESID 1610:1641)F1610 - 1641
26X-RAY DIFFRACTION26(CHAIN M AND RESID 2:27)M2 - 27
27X-RAY DIFFRACTION27(CHAIN M AND RESID 28:77)M28 - 77
28X-RAY DIFFRACTION28(CHAIN M AND RESID 78:85)M78 - 85
29X-RAY DIFFRACTION29(CHAIN P AND RESID 2:27)P2 - 27
30X-RAY DIFFRACTION30(CHAIN P AND RESID 28:77)P28 - 77
31X-RAY DIFFRACTION31(CHAIN P AND RESID 78:85)P78 - 85

+
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