[English] 日本語
Yorodumi
- PDB-9mfg: Complex of IL23 receptor and VHH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mfg
TitleComplex of IL23 receptor and VHH
Components
  • Interleukin-23 receptor
  • VHH
KeywordsIMMUNE SYSTEM / immunology / IBD / inflammatory bowel disease
Function / homology
Function and homology information


prolactin receptor activity / positive regulation of NK T cell activation / positive regulation of T-helper 1 type immune response / interleukin-23 receptor complex / interleukin-23-mediated signaling pathway / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / positive regulation of memory T cell differentiation / positive regulation of natural killer cell proliferation / positive regulation of osteoclast differentiation ...prolactin receptor activity / positive regulation of NK T cell activation / positive regulation of T-helper 1 type immune response / interleukin-23 receptor complex / interleukin-23-mediated signaling pathway / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / positive regulation of memory T cell differentiation / positive regulation of natural killer cell proliferation / positive regulation of osteoclast differentiation / cell surface receptor signaling pathway via STAT / cytokine receptor activity / positive regulation of granulocyte macrophage colony-stimulating factor production / negative regulation of interleukin-10 production / cytokine binding / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / peptide hormone binding / response to type II interferon / cell surface receptor signaling pathway via JAK-STAT / positive regulation of T-helper 17 cell lineage commitment / positive regulation of T cell proliferation / positive regulation of defense response to virus by host / positive regulation of interleukin-12 production / cytokine-mediated signaling pathway / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / receptor complex / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / cell surface / plasma membrane
Similarity search - Function
: / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
THIOCYANATE ION / Interleukin-23 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKiefer, J.R. / Wallweber, H.A. / Koerber, J.T. / Ota, N. / Davies, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Engineering a protease-stable, oral single-domain antibody to inhibit IL-23 signaling.
Authors: Ota, N. / Davies, C.W. / Kang, J. / Yan, D. / Scherl, A. / Wong, A. / Cook, R. / Tao, X. / Dunlap, D. / Klabunde, S. / Mantik, P. / Mohanan, V. / Lin, W. / McBride, J. / Sadekar, S. / ...Authors: Ota, N. / Davies, C.W. / Kang, J. / Yan, D. / Scherl, A. / Wong, A. / Cook, R. / Tao, X. / Dunlap, D. / Klabunde, S. / Mantik, P. / Mohanan, V. / Lin, W. / McBride, J. / Sadekar, S. / Storek, K.M. / Lupardus, P. / Ye, Z. / Ackerly Wallweber, H. / Kiefer, J.R. / Xu, M. / Chan, P. / Nagapudi, K. / Yi, T. / Koerber, J.T.
History
DepositionDec 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-23 receptor
B: Interleukin-23 receptor
C: Interleukin-23 receptor
D: Interleukin-23 receptor
E: VHH
F: VHH
G: VHH
H: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,83834
Polymers193,7028
Non-polymers9,13726
Water1,62190
1
A: Interleukin-23 receptor
G: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9798
Polymers48,4252
Non-polymers1,5546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint15 kcal/mol
Surface area20440 Å2
MethodPISA
2
B: Interleukin-23 receptor
H: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0667
Polymers48,4252
Non-polymers2,6405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint33 kcal/mol
Surface area21720 Å2
MethodPISA
3
C: Interleukin-23 receptor
F: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0578
Polymers48,4252
Non-polymers2,6316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint21 kcal/mol
Surface area21160 Å2
MethodPISA
4
D: Interleukin-23 receptor
E: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,73711
Polymers48,4252
Non-polymers2,3119
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint20 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.313, 403.472, 84.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein / Antibody , 2 types, 8 molecules ABCDEFGH

#1: Protein
Interleukin-23 receptor / IL-23 receptor / IL-23R


Mass: 35286.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23R / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5VWK5
#2: Antibody
VHH


Mass: 13138.472 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Cricetulus griseus (Chinese hamster)

-
Sugars , 6 types, 18 molecules

#3: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#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.: 5
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DManpa1-3[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-2-1-3/a3-b1_a6-d1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-D-Manp]{[(3+1)][b-D-GlcpNAc]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose- ...alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-2-1-3/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-D-Manp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-D-Manp]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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.: 5 / Source method: obtained synthetically / 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 , 4 types, 98 molecules

#9: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris (pH 8.5), 16% 606 PEG4000, 200 mM Li2SO4, 200 mM NaSCN and was cryoprotected with 25% glycerol

-
Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.85→35 Å / Num. obs: 74785 / % possible obs: 87.8 % / Redundancy: 3 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.077 / Rrim(I) all: 0.146 / Χ2: 1.066 / Net I/σ(I): 6 / Num. measured all: 225294
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.85-2.91.70.50719700.3950.7530.4150.6590.68547.1
2.9-2.951.80.51525010.4160.7670.420.6680.76259.7
2.95-3.0120.47728040.5160.8250.3750.610.74765.9
3.01-3.072.10.42329780.6530.8890.320.5330.78771.6
3.07-3.142.20.3933020.690.9040.2930.4910.80578
3.14-3.212.30.34634830.7880.9390.2570.4340.78882.8
3.21-3.292.40.30836890.8570.9610.2210.3810.86587.4
3.29-3.382.60.28138700.8710.9650.1960.3440.91591.9
3.38-3.482.80.25440290.9010.9740.1710.3080.92496.3
3.48-3.593.10.2440940.9310.9820.1540.2870.95297.4
3.59-3.723.20.21641570.9430.9850.1330.2560.98397.9
3.72-3.873.30.18641400.9620.990.1120.2180.99897.4
3.87-4.043.30.1641060.9720.9930.0970.1881.06196.7
4.04-4.263.10.12440240.9770.9940.080.1491.16994.4
4.26-4.523.60.1142160.9830.9960.0660.1291.1999
4.52-4.873.80.10242280.9860.9970.0580.1181.22198.9
4.87-5.363.80.09542740.9850.9960.0540.111.16699
5.36-6.133.70.09542650.9840.9960.0540.111.19198.5
6.13-7.713.50.08442630.9880.9970.0490.0981.20397.3
7.71-353.60.05743920.9930.9980.0340.0671.29195.3

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→34.97 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 3590 4.84 %
Rwork0.2039 --
obs0.206 74222 87.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12779 0 597 90 13466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513748
X-RAY DIFFRACTIONf_angle_d0.75118758
X-RAY DIFFRACTIONf_dihedral_angle_d18.2875304
X-RAY DIFFRACTIONf_chiral_restr0.0482204
X-RAY DIFFRACTIONf_plane_restr0.0052319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.890.3913690.35151365X-RAY DIFFRACTION44
2.89-2.930.38730.32121678X-RAY DIFFRACTION54
2.93-2.970.34741020.31121862X-RAY DIFFRACTION62
2.97-3.010.3344790.30522103X-RAY DIFFRACTION66
3.01-3.060.34431280.2922102X-RAY DIFFRACTION70
3.06-3.110.36761230.30532337X-RAY DIFFRACTION76
3.11-3.160.3371160.29332414X-RAY DIFFRACTION79
3.16-3.220.32481210.29232576X-RAY DIFFRACTION83
3.22-3.280.35291470.27392663X-RAY DIFFRACTION87
3.28-3.350.32011660.25572770X-RAY DIFFRACTION91
3.35-3.420.2931400.25932883X-RAY DIFFRACTION94
3.42-3.50.28771560.22942980X-RAY DIFFRACTION96
3.5-3.590.31151530.2292971X-RAY DIFFRACTION97
3.59-3.690.27511420.21843044X-RAY DIFFRACTION97
3.69-3.790.27421420.2123026X-RAY DIFFRACTION97
3.79-3.920.26351580.20223014X-RAY DIFFRACTION97
3.92-4.060.25221480.18113021X-RAY DIFFRACTION96
4.06-4.220.2081710.15522920X-RAY DIFFRACTION94
4.22-4.410.19491500.14833025X-RAY DIFFRACTION98
4.41-4.640.17511420.14463115X-RAY DIFFRACTION99
4.64-4.930.18821580.14193079X-RAY DIFFRACTION99
4.93-5.310.18431480.15163138X-RAY DIFFRACTION99
5.31-5.840.18851720.16733121X-RAY DIFFRACTION99
5.84-6.680.23871740.19193089X-RAY DIFFRACTION98
6.68-8.40.2221330.21793077X-RAY DIFFRACTION94
8.4-34.970.23081790.22643259X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.7330.53180.93032.34540.70651.567-0.1149-0.10160.20350.14590.08160.0893-0.03160.153200.57780.01280.04310.46040.06960.477846.802839.25989.536
20.84380.0644-0.00274.40790.80951.0193-0.1252-0.1751-0.1948-0.05610.09280.37350.1725-0.2745-0.00020.49440.0014-0.03160.54960.13060.673818.0559.64375.0266
30.5839-0.2894-0.65320.2408-0.85582.32980.10870.501-0.0989-0.8507-0.03550.25371.05220.0866-0.00011.2126-0.038-0.14860.77890.06360.82320.4674-7.356-20.9157
43.81140.3819-0.45362.1735-0.47322.2794-0.0562-0.112-0.17820.18410.13830.0848-0.0573-0.0952-0.00010.5288-0.0092-0.08690.4759-0.01180.5869-0.279560.25053.7864
51.30860.1825-0.12080.0809-0.03860.45220.03670.0749-0.0088-0.0113-0.07910.222-0.18660.388400.59240.0204-0.01010.646-0.02640.482718.309777.7068-12.1268
60.8324-0.9091-0.77521.55020.08621.7260.0872-0.04950.8972-0.1407-0.07990.3596-0.58490.44320.00010.7078-0.1038-0.05390.720.08110.390928.589890.1027-9.0634
71.07190.7116-0.35471.0667-0.87011.6932-0.00590.6332-0.099-0.5771-0.034-0.2360.02870.785500.92550.09770.07261.19730.01010.549531.546188.9426-40.1172
80.12440.3021-0.0067-0.0491-0.31630.525-0.08930.5980.1584-0.32590.1192-0.16270.43421.3570.00181.00950.08090.07221.08250.15550.763627.898586.2971-44.7141
94.08440.72510.7541.0479-0.8251.4986-0.07750.03380.2594-0.00940.00030.10720.1396-0.1182-00.60130.0353-0.10450.4567-0.09740.64270.809936.47258.7183
101.92450.19310.86030.44730.11361.8824-0.1181-0.2053-0.02750.01130.0604-0.04960.41720.597900.61430.10910.02620.72310.05040.431730.614115.93322.1548
11-0.30910.159-0.1397-0.73190.13630.5716-0.1169-0.39990.32420.58870.0957-0.22030.08870.79430.00031.11030.1966-0.06671.43380.03810.622837.335512.232755.8229
123.3626-0.3194-0.74413.13030.31811.6565-0.2641-0.3034-0.2975-0.13550.1735-0.00970.12230.11180.00010.54810.012-0.03220.4420.06170.375245.287762.86711.9117
131.2143-1.5836-1.13762.31350.81740.90790.03580.1918-0.16030.0383-0.07970.3686-0.0513-0.26070.00010.4838-0.0022-0.03630.570.08930.494715.283888.34026.9898
141.5616-0.49441.75620.3318-0.26891.4521-0.1788-0.63350.25810.5898-0.01020.1096-0.4721-0.1067-0.00020.84920.0740.09330.82710.06880.576711.7778106.960932.4142
152.16910.71491.49742.0003-0.49251.6752-0.1011-0.2181.3790.0527-0.0687-0.006-0.35560.0196-0.00090.5411-0.07020.01530.4159-0.12580.675862.692183.0981.2486
161.33350.4839-0.190.52360.32680.37690.01350.15370.6495-0.255-0.01320.0173-0.1977-0.8025-0.00010.56570.0338-0.00150.50310.01130.434655.67278.6019-6.0876
171.08880.7153-0.20860.6817-0.4530.37330.3356-0.4469-0.14510.2928-0.1892-0.345-0.27420.358-00.57280.0001-0.06450.4847-0.07040.451562.927974.34693.1677
183.2405-0.65322.05490.5171-0.49821.36540.81880.3693-1.4866-0.8543-0.10020.39361.0195-0.30390.0770.5903-0.00240.01740.49830.11030.4168.445474.4536-12.2239
191.26410.25561.1862.9095-0.71021.86830.0413-0.2160.28530.5009-0.1628-0.0203-0.8987-0.1153-00.55610.0636-0.0180.3761-0.03210.625256.016582.7973-2.2942
200.83970.605-0.05851.2923-0.89240.50810.178-0.7605-1.06140.39040.16990.28460.2058-0.079500.60880.0434-0.0780.62290.10020.7957-16.400118.528618.4904
210.4070.4722-0.32510.3804-0.22590.21650.06160.0936-0.52670.8413-0.1434-1.03180.78580.1638-0.00010.5440.0443-0.06160.53470.00730.739-9.445319.12149.6892
221.54240.734-0.52961.21970.08520.33090.1564-0.22040.14610.3755-0.17280.5007-0.12260.0233-0.00010.61280.0345-0.12690.5149-0.04010.5109-16.704127.101716.0091
231.0920.145-0.32530.14540.30640.40060.04840.271-0.68450.389-0.32330.46550.19390.043500.53770.0095-0.08920.52460.05440.7892-17.389918.06898.6476
240.36360.2452-0.30270.59120.01330.24050.5656-0.5392-0.67180.7573-0.4831-0.80640.42720.45330.0020.61390.0335-0.31030.56950.08110.7408-2.759619.57918.8607
250.66240.1-0.48970.0205-0.07650.3772-1.2346-0.1446-0.8325-0.2457-0.72030.9054-0.0336-0.324-0.54450.6467-0.0963-0.16550.6124-0.0350.6808-24.346511.93686.5489
261.52770.2645-1.72890.1603-0.39532.12250.1017-0.5731-1.21260.5479-0.9217-0.02990.82110.7807-0.67770.6678-0.0549-0.11630.49180.09631.391672.079821.114615.3046
271.20340.11370.4611.2772-0.02930.58930.26550.5725-1.6313-0.1430.1920.42070.0365-0.14050.00890.51190.0622-0.03880.6245-0.02890.837763.532822.61437.753
280.35730.16090.14180.34970.19630.1026-0.0011-1.1319-1.05250.38620.15920.09330.3826-0.429-0.00040.6840.0193-0.11580.75360.22280.668759.322325.005919.523
291.3526-0.293-0.23260.8218-0.53730.4761-0.053-0.2314-0.40630.18970.2483-0.4076-0.06180.2539-0.00030.4951-0.045-0.02420.47920.06060.726163.403233.01599.9491
301.3466-0.7633-0.03211.2789-0.28190.22650.0644-0.5774-0.26130.1759-0.0754-0.40390.3745-0.15330.00220.5718-0.0273-0.02430.7304-0.06680.754370.142128.332413.8745
310.133-0.0919-0.00260.12320.08830.0723-0.0725-0.5529-1.1403-0.1496-0.2653-0.39550.6477-0.0503-0.00220.5826-0.0259-0.01670.51340.12910.673162.442221.439214.7284
320.20970.0725-0.29730.1602-0.06660.3483-0.32290.0406-0.9710.17960.21371.01360.0577-0.2277-0.00010.6091-0.091-0.13430.60660.0130.946653.05721.00349.1266
330.06360.1151-0.02070.39470.15510.2197-0.988-1.0353-0.127-0.30590.9785-0.44610.00460.5180.00330.65860.2071-0.10170.8970.35920.915773.92222.933524.7723
340.6841-0.08010.47170.8797-0.15530.3069-0.3086-0.36771.86920.1709-0.3684-0.0826-0.37131.1079-0.15340.6278-0.1054-0.08210.58980.18541.2277-25.537379.5809-1.2957
351.8609-0.63960.37272.5655-0.78581.6592-0.16930.24451.02930.0305-0.0963-0.430.15040.1993-0.00010.5018-0.0436-0.09680.61860.02740.8751-16.131675.4678-2.2137
360.3109-0.0398-0.1110.6438-0.09970.02420.24220.14460.0852-0.0119-0.3670.34250.1486-0.38520.00010.571-0.0427-0.13490.57260.0540.6148-15.359965.66922.2612
370.85420.3101-0.28770.5695-0.03910.1128-0.00570.29540.318-0.22960.05920.42030.6708-0.40510.00010.60770.0044-0.09490.61320.09760.8158-22.669168.9638-4.424
380.0665-0.0653-0.03940.06390.06330.10640.40120.0130.58061.59350.4647-0.5649-0.2772-0.11210.00360.6427-0.1256-0.02470.9806-0.10640.9025-24.452476.090612.7593
390.0550.035-0.10760.0055-0.04860.1080.0259-0.06170.984-0.7716-0.43180.53-0.3301-0.07920.00010.6822-0.0246-0.07430.41270.06670.9795-16.230778.6465-1.1479
400.47980.42650.31780.6051-0.1430.64890.03451.03030.69640.2154-0.6389-0.43340.05270.0823-0.00010.5119-0.11820.12230.86250.21220.8861-6.779676.1777-5.9759
415.8424-0.44621.02490.087-0.48373.5226-0.6411-1.02850.5858-0.0730.2061-0.3307-0.5197-0.98-0.12490.8860.0677-0.23940.562-0.08711.0858-27.872682.39178.1886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 216 )
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 317 )
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 110 )
5X-RAY DIFFRACTION5chain 'B' and (resid 111 through 156 )
6X-RAY DIFFRACTION6chain 'B' and (resid 157 through 200 )
7X-RAY DIFFRACTION7chain 'B' and (resid 201 through 298 )
8X-RAY DIFFRACTION8chain 'B' and (resid 299 through 322 )
9X-RAY DIFFRACTION9chain 'C' and (resid 25 through 110 )
10X-RAY DIFFRACTION10chain 'C' and (resid 111 through 222 )
11X-RAY DIFFRACTION11chain 'C' and (resid 223 through 319 )
12X-RAY DIFFRACTION12chain 'D' and (resid 25 through 110 )
13X-RAY DIFFRACTION13chain 'D' and (resid 111 through 230 )
14X-RAY DIFFRACTION14chain 'D' and (resid 231 through 317 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 39 )
16X-RAY DIFFRACTION16chain 'E' and (resid 40 through 52 )
17X-RAY DIFFRACTION17chain 'E' and (resid 53 through 82 )
18X-RAY DIFFRACTION18chain 'E' and (resid 83 through 90 )
19X-RAY DIFFRACTION19chain 'E' and (resid 91 through 120 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 39 )
21X-RAY DIFFRACTION21chain 'F' and (resid 40 through 52 )
22X-RAY DIFFRACTION22chain 'F' and (resid 53 through 82 )
23X-RAY DIFFRACTION23chain 'F' and (resid 83 through 98 )
24X-RAY DIFFRACTION24chain 'F' and (resid 99 through 113 )
25X-RAY DIFFRACTION25chain 'F' and (resid 114 through 120 )
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 17 )
27X-RAY DIFFRACTION27chain 'G' and (resid 18 through 39 )
28X-RAY DIFFRACTION28chain 'G' and (resid 40 through 51 )
29X-RAY DIFFRACTION29chain 'G' and (resid 52 through 72 )
30X-RAY DIFFRACTION30chain 'G' and (resid 73 through 90 )
31X-RAY DIFFRACTION31chain 'G' and (resid 91 through 98 )
32X-RAY DIFFRACTION32chain 'G' and (resid 99 through 113 )
33X-RAY DIFFRACTION33chain 'G' and (resid 114 through 120 )
34X-RAY DIFFRACTION34chain 'H' and (resid 1 through 16 )
35X-RAY DIFFRACTION35chain 'H' and (resid 17 through 51 )
36X-RAY DIFFRACTION36chain 'H' and (resid 52 through 66 )
37X-RAY DIFFRACTION37chain 'H' and (resid 67 through 83 )
38X-RAY DIFFRACTION38chain 'H' and (resid 84 through 90 )
39X-RAY DIFFRACTION39chain 'H' and (resid 91 through 98 )
40X-RAY DIFFRACTION40chain 'H' and (resid 99 through 113 )
41X-RAY DIFFRACTION41chain 'H' and (resid 114 through 120 )

+
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