[English] 日本語
Yorodumi
- PDB-8s7c: Ternary Complex of Cachd1, FZD5 and LRP6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s7c
TitleTernary Complex of Cachd1, FZD5 and LRP6
Components
  • Frizzled-5
  • Low-density lipoprotein receptor-related protein 6
  • VWFA and cache domain-containing protein 1
KeywordsSIGNALING PROTEIN / Cachd1 Frizzled-5 LRP6
Function / homology
Function and homology information


regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / Wnt signaling pathway involved in somitogenesis / cellular response to molecule of bacterial origin / Disassembly of the destruction complex and recruitment of AXIN to the membrane / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / embryonic camera-type eye morphogenesis / chorionic trophoblast cell differentiation ...regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / Wnt signaling pathway involved in somitogenesis / cellular response to molecule of bacterial origin / Disassembly of the destruction complex and recruitment of AXIN to the membrane / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / embryonic camera-type eye morphogenesis / chorionic trophoblast cell differentiation / glandular epithelial cell maturation / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Asymmetric localization of PCP proteins / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / embryonic camera-type eye development / post-embryonic camera-type eye development / Ca2+ pathway / apoptotic process involved in morphogenesis / anterior/posterior axis specification, embryo / embryonic axis specification / kinase inhibitor activity / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / non-canonical Wnt signaling pathway / intestinal epithelial cell maturation / presynapse assembly / Wnt receptor activity / cellular response to cholesterol / branching involved in labyrinthine layer morphogenesis / midbrain dopaminergic neuron differentiation / Wnt-protein binding / negative regulation of protein serine/threonine kinase activity / dopaminergic neuron differentiation / frizzled binding / vasculature development / Wnt signalosome / neural crest cell differentiation / regulation of bicellular tight junction assembly / Disassembly of the destruction complex and recruitment of AXIN to the membrane / labyrinthine layer blood vessel development / voltage-gated calcium channel complex / negative regulation of smooth muscle cell apoptotic process / voltage-gated calcium channel activity / bicellular tight junction / canonical Wnt signaling pathway / coreceptor activity / positive regulation of cell cycle / Regulation of FZD by ubiquitination / positive regulation of interleukin-1 beta production / TCF dependent signaling in response to WNT / protein localization to plasma membrane / G protein-coupled receptor activity / positive regulation of T cell cytokine production / Wnt signaling pathway / response to peptide hormone / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / amyloid-beta binding / early endosome membrane / positive regulation of cytosolic calcium ion concentration / T cell differentiation in thymus / cytoplasmic vesicle / chemical synaptic transmission / perikaryon / angiogenesis / membrane raft / negative regulation of cell population proliferation / axon / Golgi membrane / signaling receptor binding / neuronal cell body / glutamatergic synapse / lipid binding / ubiquitin protein ligase binding / synapse / dendrite / protein-containing complex binding / protein kinase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Frizzled-5, CRD domain / Low density lipoprotein receptor-related protein 5/6 / Periplasmic sensor-like domain superfamily / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily ...Frizzled-5, CRD domain / Low density lipoprotein receptor-related protein 5/6 / Periplasmic sensor-like domain superfamily / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Coagulation Factor Xa inhibitory site / VWFA domain profile. / von Willebrand factor, type A / Epidermal growth factor-like domain. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 6 / VWFA and cache domain-containing protein 1 / Frizzled-5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.7 Å
AuthorsZhao, Y. / Ren, J. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
Wellcome Trust223133/Z/21/Z United Kingdom
CitationJournal: Science / Year: 2024
Title: Cachd1 interacts with Wnt receptors and regulates neuronal asymmetry in the zebrafish brain.
Authors: Powell, G.T. / Faro, A. / Zhao, Y. / Stickney, H. / Novellasdemunt, L. / Henriques, P. / Gestri, G. / Redhouse White, E. / Ren, J. / Lu, W. / Young, R.M. / Hawkins, T.A. / Cavodeassi, F. / ...Authors: Powell, G.T. / Faro, A. / Zhao, Y. / Stickney, H. / Novellasdemunt, L. / Henriques, P. / Gestri, G. / Redhouse White, E. / Ren, J. / Lu, W. / Young, R.M. / Hawkins, T.A. / Cavodeassi, F. / Schwarz, Q. / Dreosti, E. / Raible, D.W. / Li, V.S.W. / Wright, G.J. / Jones, E.Y. / Wilson, S.W.
History
DepositionFeb 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VWFA and cache domain-containing protein 1
B: Frizzled-5
C: Low-density lipoprotein receptor-related protein 6
D: VWFA and cache domain-containing protein 1
E: Frizzled-5
F: Low-density lipoprotein receptor-related protein 6
G: VWFA and cache domain-containing protein 1
H: Frizzled-5
I: Low-density lipoprotein receptor-related protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)637,94241
Polymers630,4579
Non-polymers7,48532
Water00
1
A: VWFA and cache domain-containing protein 1
B: Frizzled-5
C: Low-density lipoprotein receptor-related protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,56813
Polymers210,1523
Non-polymers2,41510
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: VWFA and cache domain-containing protein 1
E: Frizzled-5
F: Low-density lipoprotein receptor-related protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,58614
Polymers210,1523
Non-polymers2,43311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: VWFA and cache domain-containing protein 1
H: Frizzled-5
I: Low-density lipoprotein receptor-related protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,78914
Polymers210,1523
Non-polymers2,63611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)283.697, 198.236, 218.824
Angle α, β, γ (deg.)90.00, 128.07, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein VWFA and cache domain-containing protein 1 / Cache domain-containing protein 1


Mass: 123058.031 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cachd1, Kiaa1573, Vwcd1 / Production host: Homo sapiens (human) / References: UniProt: Q6PDJ1
#2: Protein Frizzled-5 / Fz-5 / mFz5


Mass: 15924.286 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fzd5 / Production host: Homo sapiens (human) / References: UniProt: Q9EQD0
#3: Protein Low-density lipoprotein receptor-related protein 6 / LRP-6


Mass: 71170.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Production host: Homo sapiens (human) / References: UniProt: O75581
#4: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 30 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 4.5
Details: 0.1 M Calcium Acetate 0.1 M Sodium Acetate 10% PEG 4000 pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 4.7→172.259 Å / Num. obs: 23514 / % possible obs: 88.8 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 6.3
Reflection shellResolution: 4.7→5.4 Å / Num. unique obs: 1177 / CC1/2: 0.437

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.7→86.13 Å / SU ML: 0.78 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1186 5.05 %
Rwork0.2063 --
obs0.2092 23464 47.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.7→86.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41238 0 476 0 41714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242599
X-RAY DIFFRACTIONf_angle_d0.57757838
X-RAY DIFFRACTIONf_dihedral_angle_d9.69715777
X-RAY DIFFRACTIONf_chiral_restr0.0496591
X-RAY DIFFRACTIONf_plane_restr0.0047456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.7-4.910.5734120.3167203X-RAY DIFFRACTION3
4.92-5.170.3495190.3085505X-RAY DIFFRACTION9
5.17-5.50.4165610.3072899X-RAY DIFFRACTION15
5.5-5.920.3808780.30861529X-RAY DIFFRACTION26
5.92-6.520.36821660.29332903X-RAY DIFFRACTION50
6.52-7.460.30382240.24844498X-RAY DIFFRACTION76
7.46-9.40.26652940.18995810X-RAY DIFFRACTION98
9.4-86.130.20933320.17395931X-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)
10.0279-0.8538-0.85831.31081.97892.3675-0.98671.6628-0.1886-0.79750.0106-0.09820.3964-0.7427-0.15990.6673-0.6103-0.72872.0004-0.1941.7951-60.6769-82.842115.6162
25.888-2.0135-2.61414.3685-3.77437.0873-0.89020.54391.101-0.5333-0.0624-1.06940.206-1.00110.26750.54650.0141-0.33991.80890.34272.061-24.6874-105.263219.7284
31.76411.37340.39241.08150.88052.855-0.5761-0.0870.9136-1.2768-0.1508-0.7357-0.34940.3212-0.26960.92590.29530.04151.65930.16181.3259-30.9645-101.95525.9867
41.8016-1.7122-0.43081.6588-0.4496.85510.55021.16020.72480.77910.0361-0.9514-2.3150.9479-0.24672.2393-0.5126-0.2471.5543-0.25241.6007-26.927-83.184350.5281
50.7136-0.34650.35871.97950.7674.0847-1.32430.04010.98450.440.1841-0.8207-0.37290.76870.20331.37470.085-0.17942.0915-0.10731.9629-22.4799-95.076861.6537
63.9160.26321.69912.9190.66290.6615-0.40650.3165-0.26020.42090.28940.34660.2370.23840.25421.2791-0.18670.29661.1659-0.13561.3504-51.4344-87.830424.9867
70.8596-0.1244-1.13011.88490.28121.7295-0.26580.04150.02180.7271-0.17630.5032-0.64340.5683-0.0681.4876-0.0183-0.18772.02780.29281.1217-56.7928-78.13062.9613
81.4853-0.88570.77776.093-0.70670.34651.10061.23060.36892.0467-0.64010.8632-0.51950.81540.19832.92090.15270.19291.6815-0.25571.2496-56.6479-56.436611.2695
96.7071.44954.58920.59290.53715.79511.7922-0.35770.77581.3647-0.81390.5017-1.9948-1.4958-1.05482.724-0.0240.62931.6730.19981.8572-53.8305-51.936726.6764
100.6778-2.15680.1155.2163-0.30131.1079-0.0789-0.40390.0648-0.83740.1849-1.9258-1.7058-0.73740.08053.0008-0.46030.49541.1682-0.44021.8364-49.5697-59.348232.0564
114.4358-3.1621-0.01092.31611.1598.1897-1.5029-2.63281.7931-1.39810.9782-1.5860.20060.53270.81481.7957-0.6209-0.03972.0652-0.12732.2677-37.7412-55.67350.7245
126.08261.83380.5955.50182.10996.7754-2.817-0.6911.5602-0.3839-1.44480.8243-1.0416-1.64333.84182.14220.86650.34563.0272-0.75182.5642-51.3554-30.871452.3781
133.51032.67863.4792.33932.64833.444-2.34990.9026-0.8091-0.9645-1.34830.5356-0.4849-1.35993.1092.37740.66130.86192.4709-0.02271.4421-45.9505-39.267852.028
143.00612.51070.27745.53832.43633.98970.14081.44650.6873-6.6020.49641.38121.0433-0.5983-0.38155.05840.9212-0.31881.05170.69612.9335-47.4047-28.692343.8707
157.45632.6938-0.81051.9991-8.94289.61321.76532.06481.3454-5.94261.52590.2325-3.2653-0.679-1.08835.03360.13340.57572.212-0.60062.1728-44.5674-43.769542.4656
163.37213.0121-4.30282.6982-3.88965.8308-0.15313.37731.662-1.14971.8132-2.3166-1.3581-0.33120.01174.7324-0.2478-0.35863.59780.09912.9858-39.6269-38.197945.6117
174.6776-1.2562-0.95076.2607-0.97882.48243.65330.06772.8196-2.4654-0.597-1.9794-2.7798-0.7999-1.46213.95760.12360.28271.6991-1.12832.1223-38.9005-25.020752.668
181.9969-5.3073-7.82055.55163.43615.7158-2.3717-1.743-3.3812.9141-1.1679-0.52630.34921.23120.452.53090.1171-0.65393.14-0.55452.0647-30.3998-44.260840.169
199.69614.37750.45795.5546-5.33819.1153-2.19511.0831-1.77361.39671.1163-0.0505-0.70540.94671.61632.5145-0.56011.06042.74520.05412.2314-37.4384-45.091233.4525
207.45181.27733.6293.70710.19442.6073-0.04541.4257-0.41170.249-0.5291.79420.4105-1.19380.6141.5337-0.29251.28723.3715-1.04242.7787-32.3599-32.726836.7477
210.74370.24860.88078.4578-1.33361.41760.15991.31840.48812.00110.10240.6024-1.3263-0.598-0.03210.89070.93011.12152.61090.67971.7978-41.5722-135.961827.3146
223.66010.39950.67072.5461-1.51752.7777-1.38770.06160.1156-0.26070.36431.3951.1302-0.3392-0.00870.8403-0.15160.66162.0306-0.30891.2225-28.1911-138.908232.2304
231.392-0.89621.29815.4132-1.27956.7285-1.2870.23041.4436-1.14050.68690.79881.03750.4482-0.12381.0791-0.0639-0.28761.5622-0.03251.6202-19.2781-137.022424.1006
240.6027-0.3311.68372.410.45735.5399-0.33630.3061-0.69780.1749-0.9815-1.2339-1.0424-0.0182-0.52730.3665-0.46810.03971.49690.10771.5866-23.005-133.226913.0002
251.72070.3824-1.77631.67460.81932.9228-0.0020.51431.2703-0.50010.1577-0.6149-1.4202-0.5347-0.01871.27770.14250.0321.88490.22861.0891-36.3399-128.080511.0414
261.8972-0.35510.09191.91780.79390.1739-1.06370.6695-0.4596-0.46950.49260.0412-0.266-0.99220.22911.7512-0.3132-0.24781.63140.15921.1483-19.9242-148.683432.4728
271.2986-0.8929-2.65349.96911.23516.3099-1.1017-0.04880.76462.64830.88390.63392.0453-0.1575-1.15251.06250.5225-0.60781.65730.35871.3493-18.4454-139.657453.2244
283.9659-0.6784-2.14872.7296-1.7844.36010.0766-0.3459-0.67881.15031.4243-1.265-1.38040.5237-0.78962.0994-0.309-0.39921.8359-0.0941.3829-14.6339-139.485470.3234
292.94282.1912.01927.4415-0.44591.8669-0.2129-0.2540.61761.2966-0.1576-0.4753-0.97520.15140.20891.52770.0616-0.19312.09060.17761.9799-1.2108-133.953559.6953
301.6162-1.4794-2.07481.2911.83642.4611-0.4294-0.2724-1.51721.1162-0.87180.78971.1107-0.25971.36282.09290.2962-0.52712.42410.26822.0397-10.8489-155.398578.443
310.65260.5551.66813.6523-1.00822.79550.35260.1013-1.8127-1.70560.5152-0.17171.32470.37450.49620.28250.65290.57181.8101-0.14661.8215-90.645-115.398532.3446
320.44080.7690.55121.00561.78963.61970.0409-0.10710.02081.2597-0.2347-0.67090.3339-0.1072-0.06571.49570.2395-0.14771.31330.07881.4423-110.8631-90.067944.6166
331.00590.9636-0.70952.77491.21253.2125-0.2656-0.44380.08210.0310.4948-0.13020.2917-1.6467-0.00031.4842-0.1297-0.27471.8676-0.05781.1865-110.8966-81.379441.9972
341.1295-0.618-1.37461.39830.72661.72460.17830.1257-0.11960.6777-0.45530.97160.70340.19730.10471.87210.02530.24311.29070.06531.8011-82.3255-124.859942.6628
351.633-0.38860.62113.44713.36995.9469-0.2151-0.1733-0.5425-0.208-0.1263-0.03420.7983-0.57810.31161.15710.19540.07311.84070.20841.6931-92.1395-128.371864.1339
362.1162-4.2999-0.36359.3828-0.64452.72882.0601-0.243-2.1662-3.37610.9307-1.9618-2.544-0.001-1.92612.9658-0.4284-0.63022.79520.35012.5317-88.6554-110.947797.5013
370.82880.8816-0.770.9371-0.8220.85760.04181.87192.2717-1.5168-1.26740.34141.9402-0.31970.45844.02580.5087-0.23022.19710.62792.4468-90.1806-121.32998.9867
383.05070.0107-0.59813.66182.07243.93470.9150.5429-1.64330.53441.30130.7488-4.3133-1.1373-1.56333.61620.0354-0.58622.01550.17061.9033-94.4308-114.708587.2901
391.26040.3028-2.05550.056-0.50093.3021-0.111-0.66650.67762.69680.59110.79013.6175-1.30460.41623.7947-0.44430.03521.8585-0.03851.2669-103.1173-115.438194.5669
405.86294.0971-3.09683.9518-3.52833.34310.05670.9408-0.84070.53920.91211.6673-0.077-0.728-0.06192.6997-1.70840.82011.8132-0.382.3825-100.9296-121.568579.7827
415.58983.65782.13971.9962-3.05363.37661.56930.5761-0.79910.05031.36582.33331.7614-1.1441.9741.4114-0.9746-0.09023.7789-0.06651.2794-105.4578-124.847892.4714
421.77971.02771.13442.0585-0.61852.96541.2758-0.62950.53260.2180.1941-0.68530.21261.34080.5566-0.62360.42580.56362.04120.50652.1815-98.5252-82.1311-2.142
433.5022-1.02472.26050.611-0.55541.49370.53630.1552-0.3759-0.3502-0.076-0.34880.7341.24560.00290.8586-0.41440.41371.5574-0.29581.4087-116.34-79.4424-2.2093
441.4247-2.15451.85843.3522-2.5476.9497-0.32871.64790.7665-0.4247-0.3334-1.37530.49710.57880.09530.8437-0.2747-0.15232.1078-0.30371.9509-117.563-96.8116-5.2547
454.7599-1.1241-2.03412.0478-2.63515.30030.906-0.4933-0.59631.51320.22990.115-0.91120.7509-0.16690.47160.01290.67971.6979-0.58661.8386-103.4697-94.4186-6.3539
461.0311.9406-0.56353.5476-1.41428.6654-0.92080.24142.5127-0.442-0.37210.3463-0.6999-3.574-0.731-0.0209-0.1835-0.17212.0132-0.92042.6161-123.9699-68.3274-14.1531
470.355-1.3114-0.42236.44493.65582.54490.4897-0.7128-0.2815-0.0761-1.67610.31131.3395-0.70350.34820.5326-0.0908-0.15341.5187-0.21071.1082-125.8329-47.789316.759
483.412-0.57551.04523.91591.64361.5758-0.47120.4018-1.35341.43890.9121.6426-0.6748-0.66020.51030.7771-0.1070.76252.5030.52721.6408-134.2683-58.202712.8489
492.97522.2492-0.75153.23850.33933.8018-0.20890.26621.1656-0.8595-1.07391.7918-2.43510.57070.33751.12130.09890.24491.5181-0.08141.73-125.0987-26.01538.1678
500.16520.77360.14254.0869-1.80151.2215-0.7208-0.5968-0.2990.6031-0.12280.0285-1.00070.2809-0.2651.49590.0264-0.00831.458-0.40791.3714-56.62783.4397106.7187
512.7971.0553-0.08231.30940.93584.95340.2831-0.3919-0.03461.0593-0.2848-0.3079-0.66341.13220.35991.18880.07170.24731.60370.02321.5409-25.22825.514282.6912
524.63132.0911.53884.6488-0.38916.25750.7093-0.1119-0.54361.8202-1.3402-0.43040.12221.09320.66821.48090.97260.16530.9940.59221.5948-26.0484-26.568386.6323
533.69931.63752.49583.97220.58064.2572-1.18210.6868-1.80260.28070.6985-0.73030.38150.5970.23591.01351.16450.07851.84870.71051.514-25.5406-33.284179.4109
541.2854-0.99140.07282.5997-0.23490.99010.0349-0.24940.11170.8971-0.0111-0.1686-0.0251-0.0290.2031.5517-0.3112-0.29941.03980.0591.2158-46.6136-2.6198104.2632
553.8476-3.8263-0.59843.77921.26513.5162-0.4648-1.0781-1.65811.1017-0.02391.07570.8489-0.27990.13512.9451-0.35010.41781.19980.25831.2581-49.4538-22.1131127.2648
561.5781-1.1295-2.20773.83611.25492.85270.39240.1942-0.59740.930.39610.1604-0.4102-0.4257-0.1983.1802-0.09430.04561.1730.31092.1632-45.8885-23.1803117.9766
572.27052.44062.72963.38253.35423.47430.2937-0.74710.0290.43881.1964-2.67820.96841.359-1.46192.4301-0.116-0.39972.1094-0.11452.8668-31.37131.2847135.8293
580.4502-0.0515-0.32940.0221-0.18212.4917-2.1188-1.0634-0.821-0.61221.5521.5427-1.06170.54660.28832.734-0.73990.58522.0301-0.42132.2056-44.7446-53.1076130.5931
595.33162.2159-3.67789.0043-3.58476.8511.5897-0.28120.27454.37520.4355-1.45041.7071-0.08520.90173.3291-1.10760.44091.44930.10892.1398-42.816-41.218132.239
603.217-0.6732-0.50690.9034-2.30617.32-0.7005-0.07430.33674.3228-1.1042-2.89470.7192-1.60280.59923.1367-0.8573-0.20331.51490.04622.6335-34.9228-51.4962130.7037
610.27570.0517-0.20232.232-2.09052.1786-1.41090.0804-0.3280.2574-0.6418-3.02-0.93131.00860.9191.8227-0.3116-0.84082.52521.02573.1741-28.2433-37.7946128.5459
620.2152-1.0796-0.01215.00480.48330.7435-0.29150.81180.36050.6958-0.05381.31870.53480.24060.07830.54250.1676-0.11542.02150.31271.8404-40.199719.117253.5081
632.6168-0.5585-0.23363.97161.48141.1829-0.76712.45182.27540.46660.75181.5272-0.4782-0.4684-0.00791.1819-0.1732-0.34391.10030.63511.9081-27.554815.353747.4693
640.48440.7624-1.06452.2482-1.04132.4644-0.16210.3850.08060.6263-0.6559-0.48990.62760.81880.17120.9082-0.1776-0.85432.00450.47521.1654-18.929524.53156.8055
650.81811.8496-0.18595.1722-0.04520.5780.312-0.45-0.65590.9372-0.61450.0146-0.85930.20880.17041.8531-1.2734-1.94250.5542-0.59351.9063-28.655830.819466.6126
662.54070.8668-1.62111.331-0.47770.990.4818-0.22760.18380.35490.41220.06570.74020.6961-0.09131.0321-0.1038-0.36451.3633-0.13861.5424-31.923428.187755.6762
672.4349-2.70071.54335.3962-0.8563.25320.1196-0.7335-0.1885-0.5977-0.3058-0.82820.1570.31970.09751.5040.62060.58171.87120.36610.8526-18.8495-1.460633.267
681.14790.07050.16560.6431.56363.7017-0.1324-0.53320.9248-0.5279-1.3132-1.85952.70280.8740.81021.9080.61440.2052.16880.62162.2304-15.5123-22.870426.666
694.0892-2.04310.52393.0006-1.09141.62040.02981.4750.1156-0.0319-1.6496-0.1342-0.03852.3366-0.0541.31930.9860.24652.46830.20842.4747-2.1841-20.390833.6737
702.46180.7064-1.45792.51912.50414.1250.59330.0819-0.3936-0.05990.1173-0.20491.46580.9417-0.19961.70020.52780.14841.97030.37781.9448-9.1249-10.10826.5646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 182 )
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 340 )
5X-RAY DIFFRACTION5chain 'A' and (resid 341 through 436 )
6X-RAY DIFFRACTION6chain 'A' and (resid 437 through 678 )
7X-RAY DIFFRACTION7chain 'A' and (resid 679 through 787 )
8X-RAY DIFFRACTION8chain 'A' and (resid 788 through 865 )
9X-RAY DIFFRACTION9chain 'A' and (resid 866 through 942 )
10X-RAY DIFFRACTION10chain 'A' and (resid 943 through 1015 )
11X-RAY DIFFRACTION11chain 'A' and (resid 1016 through 1088 )
12X-RAY DIFFRACTION12chain 'B' and (resid 32 through 38 )
13X-RAY DIFFRACTION13chain 'B' and (resid 39 through 46 )
14X-RAY DIFFRACTION14chain 'B' and (resid 47 through 59 )
15X-RAY DIFFRACTION15chain 'B' and (resid 60 through 81 )
16X-RAY DIFFRACTION16chain 'B' and (resid 82 through 90 )
17X-RAY DIFFRACTION17chain 'B' and (resid 91 through 105 )
18X-RAY DIFFRACTION18chain 'B' and (resid 106 through 122 )
19X-RAY DIFFRACTION19chain 'B' and (resid 123 through 128 )
20X-RAY DIFFRACTION20chain 'B' and (resid 129 through 135 )
21X-RAY DIFFRACTION21chain 'C' and (resid 630 through 690 )
22X-RAY DIFFRACTION22chain 'C' and (resid 691 through 733 )
23X-RAY DIFFRACTION23chain 'C' and (resid 734 through 777 )
24X-RAY DIFFRACTION24chain 'C' and (resid 778 through 819 )
25X-RAY DIFFRACTION25chain 'C' and (resid 820 through 878 )
26X-RAY DIFFRACTION26chain 'C' and (resid 879 through 947 )
27X-RAY DIFFRACTION27chain 'C' and (resid 948 through 993 )
28X-RAY DIFFRACTION28chain 'C' and (resid 994 through 1081 )
29X-RAY DIFFRACTION29chain 'C' and (resid 1082 through 1203 )
30X-RAY DIFFRACTION30chain 'C' and (resid 1204 through 1246 )
31X-RAY DIFFRACTION31chain 'D' and (resid 53 through 168 )
32X-RAY DIFFRACTION32chain 'D' and (resid 169 through 369 )
33X-RAY DIFFRACTION33chain 'D' and (resid 370 through 506 )
34X-RAY DIFFRACTION34chain 'D' and (resid 507 through 865 )
35X-RAY DIFFRACTION35chain 'D' and (resid 866 through 1088 )
36X-RAY DIFFRACTION36chain 'E' and (resid 32 through 46 )
37X-RAY DIFFRACTION37chain 'E' and (resid 47 through 59 )
38X-RAY DIFFRACTION38chain 'E' and (resid 60 through 90 )
39X-RAY DIFFRACTION39chain 'E' and (resid 91 through 122 )
40X-RAY DIFFRACTION40chain 'E' and (resid 123 through 128 )
41X-RAY DIFFRACTION41chain 'E' and (resid 129 through 135 )
42X-RAY DIFFRACTION42chain 'F' and (resid 630 through 690 )
43X-RAY DIFFRACTION43chain 'F' and (resid 691 through 777 )
44X-RAY DIFFRACTION44chain 'F' and (resid 778 through 834 )
45X-RAY DIFFRACTION45chain 'F' and (resid 835 through 896 )
46X-RAY DIFFRACTION46chain 'F' and (resid 897 through 930 )
47X-RAY DIFFRACTION47chain 'F' and (resid 931 through 1146 )
48X-RAY DIFFRACTION48chain 'F' and (resid 1147 through 1203 )
49X-RAY DIFFRACTION49chain 'F' and (resid 1204 through 1246 )
50X-RAY DIFFRACTION50chain 'G' and (resid 53 through 129 )
51X-RAY DIFFRACTION51chain 'G' and (resid 130 through 239 )
52X-RAY DIFFRACTION52chain 'G' and (resid 240 through 304 )
53X-RAY DIFFRACTION53chain 'G' and (resid 305 through 386 )
54X-RAY DIFFRACTION54chain 'G' and (resid 387 through 865 )
55X-RAY DIFFRACTION55chain 'G' and (resid 866 through 942 )
56X-RAY DIFFRACTION56chain 'G' and (resid 943 through 1015 )
57X-RAY DIFFRACTION57chain 'G' and (resid 1016 through 1088 )
58X-RAY DIFFRACTION58chain 'H' and (resid 32 through 51 )
59X-RAY DIFFRACTION59chain 'H' and (resid 52 through 76 )
60X-RAY DIFFRACTION60chain 'H' and (resid 77 through 105 )
61X-RAY DIFFRACTION61chain 'H' and (resid 106 through 135 )
62X-RAY DIFFRACTION62chain 'I' and (resid 630 through 690 )
63X-RAY DIFFRACTION63chain 'I' and (resid 691 through 733 )
64X-RAY DIFFRACTION64chain 'I' and (resid 734 through 819 )
65X-RAY DIFFRACTION65chain 'I' and (resid 820 through 849 )
66X-RAY DIFFRACTION66chain 'I' and (resid 850 through 911 )
67X-RAY DIFFRACTION67chain 'I' and (resid 912 through 1032 )
68X-RAY DIFFRACTION68chain 'I' and (resid 1033 through 1081 )
69X-RAY DIFFRACTION69chain 'I' and (resid 1082 through 1146 )
70X-RAY DIFFRACTION70chain 'I' and (resid 1147 through 1246 )

+
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://pdbjlvh1.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