[English] 日本語
Yorodumi
- PDB-4y5v: Diabody 305 complex with EpoR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y5v
TitleDiabody 305 complex with EpoR
Components
  • Diabody 305 VL domain
  • Erythropoietin receptor
  • diabody 305 VH domain
Keywordsprotein binding/immune system / diabody complex / receptor / protein binding-immune system complex
Function / homology
Function and homology information


erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway ...erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway / heart development / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.604 Å
AuthorsMoraga, I. / Guo, F. / Ozkan, E. / Jude, K.M. / Garcia, K.C.
CitationJournal: Cell / Year: 2015
Title: Tuning Cytokine Receptor Signaling by Re-orienting Dimer Geometry with Surrogate Ligands.
Authors: Moraga, I. / Wernig, G. / Wilmes, S. / Gryshkova, V. / Richter, C.P. / Hong, W.J. / Sinha, R. / Guo, F. / Fabionar, H. / Wehrman, T.S. / Krutzik, P. / Demharter, S. / Plo, I. / Weissman, I.L. ...Authors: Moraga, I. / Wernig, G. / Wilmes, S. / Gryshkova, V. / Richter, C.P. / Hong, W.J. / Sinha, R. / Guo, F. / Fabionar, H. / Wehrman, T.S. / Krutzik, P. / Demharter, S. / Plo, I. / Weissman, I.L. / Minary, P. / Majeti, R. / Constantinescu, S.N. / Piehler, J. / Garcia, K.C.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: diabody 305 VH domain
B: Diabody 305 VL domain
C: Erythropoietin receptor
D: diabody 305 VH domain
E: Diabody 305 VL domain
F: Erythropoietin receptor
G: diabody 305 VH domain
H: Diabody 305 VL domain
I: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,72126
Polymers153,0849
Non-polymers1,63817
Water5,423301
1
A: diabody 305 VH domain
B: Diabody 305 VL domain
C: Erythropoietin receptor
D: diabody 305 VH domain
E: Diabody 305 VL domain
F: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,23318
Polymers102,0566
Non-polymers1,17712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: diabody 305 VH domain
H: Diabody 305 VL domain
I: Erythropoietin receptor
hetero molecules

G: diabody 305 VH domain
H: Diabody 305 VL domain
I: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,97716
Polymers102,0566
Non-polymers92110
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Unit cell
Length a, b, c (Å)125.730, 215.021, 171.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 3 molecules CFI

#3: Protein Erythropoietin receptor / EPO-R


Mass: 25129.424 Da / Num. of mol.: 3 / Mutation: N52Q, N164Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPOR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19235

-
Antibody , 2 types, 6 molecules ADGBEH

#1: Antibody diabody 305 VH domain


Mass: 13819.239 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody Diabody 305 VL domain


Mass: 12079.210 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

-
Non-polymers , 4 types, 318 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→45.576 Å / Num. obs: 68355 / % possible obs: 96 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 13.6
Reflection shellResolution: 2.604→2.697 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.7 / % possible all: 77.43

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.604→45.576 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 3457 5.06 %
Rwork0.1867 --
obs0.1888 68333 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.604→45.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9851 0 107 301 10259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210235
X-RAY DIFFRACTIONf_angle_d0.6513895
X-RAY DIFFRACTIONf_dihedral_angle_d9.7053609
X-RAY DIFFRACTIONf_chiral_restr0.0261515
X-RAY DIFFRACTIONf_plane_restr0.0031763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6042-2.63990.30431110.2591987X-RAY DIFFRACTION74
2.6399-2.67760.30211250.25862080X-RAY DIFFRACTION78
2.6776-2.71750.31251070.24992238X-RAY DIFFRACTION83
2.7175-2.760.32911180.2422313X-RAY DIFFRACTION86
2.76-2.80520.30111280.2342386X-RAY DIFFRACTION89
2.8052-2.85360.27721310.24682515X-RAY DIFFRACTION93
2.8536-2.90550.30061440.24572566X-RAY DIFFRACTION96
2.9055-2.96140.28531430.23712623X-RAY DIFFRACTION98
2.9614-3.02180.27371380.23832642X-RAY DIFFRACTION99
3.0218-3.08750.29461410.22732675X-RAY DIFFRACTION99
3.0875-3.15930.25551300.20922698X-RAY DIFFRACTION100
3.1593-3.23830.26651470.19912686X-RAY DIFFRACTION100
3.2383-3.32580.22551410.19322697X-RAY DIFFRACTION100
3.3258-3.42360.25361430.19492709X-RAY DIFFRACTION100
3.4236-3.53410.22521410.19222699X-RAY DIFFRACTION100
3.5341-3.66040.22841430.17772713X-RAY DIFFRACTION100
3.6604-3.80680.24261430.17542695X-RAY DIFFRACTION100
3.8068-3.980.19981410.17212701X-RAY DIFFRACTION100
3.98-4.18970.20881380.15722733X-RAY DIFFRACTION100
4.1897-4.4520.17151480.14442715X-RAY DIFFRACTION100
4.452-4.79540.17921410.13892715X-RAY DIFFRACTION100
4.7954-5.27730.20411610.14912704X-RAY DIFFRACTION100
5.2773-6.03950.19611620.17492747X-RAY DIFFRACTION100
6.0395-7.60340.2451380.20212770X-RAY DIFFRACTION100
7.6034-45.5830.20261540.1922869X-RAY DIFFRACTION99
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)
15.91192.72112.12933.3710.97154.5739-0.04750.54310.1144-0.60280.20750.3209-0.12140.2059-0.16150.49580.0327-0.05280.18130.02680.3443-62.0509-49.2532-63.9273
23.8468-1.45110.35923.6074-0.733.86320.0435-0.1862-0.0307-0.05390.06890.1526-0.2688-0.2867-0.07570.29080.0093-0.04120.1919-0.03480.2232-63.0547-53.883-56.5494
33.12172.46630.89497.43322.42034.9239-0.15180.0836-0.0588-0.6130.1568-0.3163-0.2320.2081-0.05210.27880.0238-0.03120.21090.01230.2582-55.5783-52.7774-58.6562
46.9166-0.0799-0.06966.698-1.41476.102-0.3335-0.18211.33040.0105-0.377-0.0024-0.1571-0.09850.46460.5530.1874-0.06140.4219-0.11680.5219-48.7026-68.0231-52.1558
53.41391.1346-0.7546.72324.23723.8129-0.54910.0738-0.721-0.66440.4389-1.64021.22791.91520.10641.01540.41360.15320.80410.0330.657-35.9599-74.4218-68.8873
61.4065-0.520.8251.3624-0.71071.94560.0582-0.0796-0.40080.3048-0.0083-0.02510.34480.2084-0.02650.6560.10430.03660.2808-0.01140.4062-53.8442-72.5926-59.2578
76.258-0.4851.37692.76611.67163.5349-0.420.62440.1625-0.92470.705-0.5463-0.06360.7785-0.3480.60170.02140.05640.3484-0.0440.2831-49.265-61.6446-69.2871
86.7711.0363-0.03672.9056-0.62462.6260.52151.0428-0.6091-0.8516-0.35870.08240.7412-0.2396-0.00670.95820.0942-0.04090.3972-0.130.3958-55.3515-73.0662-72.8434
91.3642-0.1692-1.25670.98540.16696.0936-0.04110.1447-0.3745-0.3378-0.0413-0.3030.68890.08410.11360.82120.1552-0.05090.3538-0.06690.4194-50.5019-77.5002-63.4516
107.3511-0.6987-3.87672.28542.03483.54510.31590.78890.2801-1.19480.2745-1.36590.72651.0499-0.49750.81910.19710.20050.5433-0.05060.633-40.034-68.9065-73.5925
112.25920.7153-1.44561.96290.41822.7579-0.1663-0.00130.1497-0.15330.22610.04190.53990.1497-0.0740.48870.0906-0.08330.28420.00290.3228-54.9088-66.7438-56.7774
122.94284.2218-1.86856.7897-3.49292.1041-0.2634-0.47240.0262-0.0340.5290.0675-0.53960.7072-0.05170.61950.16110.07390.6792-0.20220.5907-35.5396-67.7926-67.1577
132.82350.4120.74222.10050.34994.9787-0.24580.3782-0.2586-0.33930.09960.14540.0218-0.52090.18870.8172-0.2062-0.14060.4985-0.06770.493-80.7645-79.3217-70.1653
140.7904-0.81720.35810.77650.31482.63920.00690.2576-0.2301-0.2923-0.14510.49570.4255-0.47970.12980.8161-0.166-0.20620.462-0.05160.5852-80.3802-77.9678-69.4389
155.10051.3188-0.78924.88290.05644.763-0.0476-0.0318-0.0518-0.0005-0.18090.07540.11-0.21280.15130.7165-0.2202-0.080.3742-0.05640.4884-81.1478-80.9955-39.4115
161.87951.296-3.8774.3333-2.38627.23050.06680.12980.21230.42010.1320.57040.015-0.3292-0.17920.9017-0.3548-0.04680.548-0.06150.5185-85.6696-82.3271-42.3206
174.04865.17512.58237.65612.90261.81580.1492-0.53360.17891.59310.2057-0.1288-0.3508-0.3988-0.42440.5231-0.0247-0.01630.4714-0.10590.4654-47.54-30.8058-14.5946
186.1396-2.035-3.74626.7179-2.52394.6350.30110.11580.38110.099-0.66270.47231.1839-1.5763-0.15560.3588-0.109-0.04160.3049-0.02070.3695-54.6395-41.772-34.5527
192.51320.20470.42846.69732.71094.8715-0.0487-0.47130.03560.78180.07010.14180.1002-0.00170.00590.2971-0.06540.02260.319-0.04190.2237-45.9829-28.0304-23.0791
205.4095-7.17560.18139.4681-0.22670.01010.353-0.81620.9877-0.14310.1394-1.32760.14860.2784-0.29530.2331-0.02870.05090.4187-0.11760.3692-41.2034-27.4975-30.2376
218.4925-4.7814-4.95525.17475.19265.30890.14140.16450.6557-0.33020.2539-0.4132-0.2162-0.1326-0.72670.4710.06170.03760.2925-0.03250.3188-46.0672-20.493-32.6778
222.3116-1.2761-0.31335.60753.37427.24950.30470.570.2902-0.4021-0.5232-0.07870.1826-0.59070.24990.2960.0026-0.0220.42630.06010.2806-51.0327-25.8905-32.4413
231.6895-2.9587-3.20165.17745.58326.0542-0.20790.0073-0.0791-0.0296-0.09290.6599-0.4131-0.43770.220.2861-0.02980.00260.4398-0.07870.2569-54.3823-26.2115-24.0134
242.8615-3.51083.26315.2843-5.13745.0435-0.2304-0.0557-0.3489-0.521-0.2494-0.05360.609-0.19780.64080.29490.0269-0.01830.3098-0.03260.344-48.2561-37.7791-38.8039
254.00820.577-1.06686.932-0.19513.18980.3014-0.16240.21990.1166-0.0549-0.0155-0.10.083-0.25730.2794-0.0607-0.03750.2806-0.00730.2416-40.0377-27.6811-21.324
267.14613.55723.31759.37596.92315.2701-0.2751-0.2252-0.28370.4502-0.39010.18391.25330.20170.23030.5761-0.15340.02310.2173-0.01830.4409-48.1412-42.3802-28.9228
275.48362.6697-4.26797.14071.88096.012-0.13150.01-0.861-1.16780.0908-0.1634-0.2378-0.59750.19510.40460.08760.00620.5619-0.16120.4325-27.6773-32.1656-34.4577
280.0254-0.06260.32821.1129-2.1496.37011.0101-0.5851-0.50210.74220.0289-0.51780.49531.0955-0.7340.36860.1723-0.1681.07080.00490.5517-15.6923-40.4068-18.2304
291.1593-0.18440.34723.07-0.92343.4351-0.0920.39270.1838-0.1547-0.1851-0.8562-0.02320.64680.31910.2768-0.1026-0.07620.56950.0080.4883-26.0291-25.5605-27.3053
305.311-3.55990.37023.38941.74775.36730.0121-0.5543-1.07060.4091-0.27770.05830.52220.28680.01140.504-0.0743-0.12330.405-0.01850.4534-33.0868-35.08-17.2122
313.8933-0.3378-2.11494.1801-0.79452.1117-0.1931-0.7440.16750.64530.523-0.2786-0.28371.384-0.17740.4211-0.1359-0.20960.8044-0.06440.4898-24.3367-24.4764-15.792
322.073-1.18221.03956.314-1.3594.2582-0.4670.2233-0.36181.04520.4079-0.6975-0.26860.34690.13560.320.0061-0.07880.78420.06060.5251-21.009-33.9401-18.6289
332.5858-0.83381.53984.7048-2.02374.86150.2492-0.1066-0.17860.33290.05640.4703-0.37370.5348-0.22880.2589-0.06440.02120.457-0.04860.3344-31.6784-27.4224-29.7041
344.7477-2.33021.63394.4619-4.19834.19920.5278-0.3103-0.88530.08850.6788-1.30082.2421.1246-1.11110.83630.2498-0.18920.7443-0.08090.664-21.0693-43.9825-19.8137
351.96240.33161.2493.1011.88665.5128-0.01970.14270.20830.22990.0922-0.0811-0.8295-0.1714-0.02980.9013-0.15870.04630.4653-0.08190.4451-33.52181.5131-16.0793
365.02181.3439-2.52759.0996-5.06896.0879-0.14630.4010.4834-0.84110.5562-1.2751-1.13410.715-0.40311.1862-0.3959-0.08240.7474-0.14630.596-29.06646.5075-10.2287
370.4750.82160.45751.36190.35793.9013-0.17230.11270.16670.10590.0065-0.1291-0.3095-0.29160.12880.5996-0.12240.00070.4781-0.08070.4342-35.0115-1.3012-26.0297
385.29940.78960.55918.6198-0.63394.6353-0.114-0.0515-0.09850.09240.00110.1929-0.3635-0.03140.12450.7185-0.31360.05230.5193-0.06470.4157-33.39532.7167-41.0658
393.92450.81270.84587.3921-3.96914.4693-0.41990.59670.05690.07140.17350.067-0.4515-0.27930.13740.8071-0.3508-0.0190.5671-0.06750.5356-35.59375.4203-51.7046
401.42971.3189-0.1594.4927-5.54688.22520.22430.05150.3834-0.04740.2340.8205-0.3650.1545-0.24950.8712-0.30380.00180.5039-0.04870.5553-32.9315.9353-40.4812
416.05410.9638-5.88432.0295-1.38635.88040.41781.18760.3226-1.2150.0101-0.2435-0.1702-0.7678-0.54340.9021-0.18560.04890.46970.01910.4121-51.4375-25.0018-71.5763
425.204-0.50715.18598.5961.33635.5792-0.297-1.0043-0.84250.54-0.05040.45-0.0321-0.20660.04580.1598-0.02570.05670.47390.11290.3423-64.1772-25.5303-51.4546
432.6678-0.0661-0.75152.3253-0.00932.9725-0.04650.4892-0.0984-0.74910.0193-0.28960.0981-0.02310.05780.4988-0.1340.15190.3805-0.06630.302-47.7697-24.0742-61.611
444.6574-5.8733-6.47297.99388.36669.81290.2964-0.717-0.0859-1.05640.4584-1.138-0.30381.321-0.62160.6085-0.02380.13340.3517-0.07330.5588-41.5589-28.9125-53.7628
452.5888-0.7771-1.67212.75261.0474.93490.00260.3166-0.5652-0.2845-0.093-0.10850.3954-0.61780.1410.4259-0.12540.07040.2762-0.06470.3068-49.7815-31.9151-58.2065
465.23681.2583-1.88932.7332-0.22992.0417-0.15020.4404-0.017-0.24290.0914-0.0488-0.2994-0.14080.00120.414-0.03840.07270.2839-0.04770.2456-52.0566-20.5362-58.6527
472.3621-3.81152.10480.14459.28830.0128-0.40970.08750.53760.16170.80.2409-0.0724-0.03890.7079-0.17490.20730.3742-0.0470.4911-42.2058-7.059-51.9552
481.5308-0.2151-0.62270.435-0.96753.013-0.26910.80020.99480.07430.247-0.3467-1.20880.30980.00511.5333-0.58850.10010.39650.13420.4972-43.35837.5603-68.205
492.12670.5901-0.38661.93860.17212.5311-0.15120.29030.3114-0.41960.1194-0.2479-0.50950.27070.01260.649-0.28560.13930.4779-0.030.4159-39.2211-7.7568-63.9704
502.3945-0.9593-2.20741.71051.62052.7404-0.8701-0.2734-0.15450.5962-0.0458-0.17312.13530.9750.36861.27340.24790.58951.01320.06680.6324-18.5757-29.6306-72.0148
513.5393-1.76922.79553.752-1.56112.3005-0.06960.22810.1431-1.4094-0.8921-1.06770.65411.43180.620.35790.16170.31191.33680.17880.8506-15.1421-28.0106-41.6733
520.2427-0.45630.38730.7503-0.5580.23440.13950.6453-0.1443-0.873-0.3964-0.97061.04181.0479-0.09170.70330.26320.42261.4390.28761.0915-13.1471-31.9525-45.5236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 118 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 8 )
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 17 )
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 40 )
7X-RAY DIFFRACTION7chain 'B' and (resid 41 through 50 )
8X-RAY DIFFRACTION8chain 'B' and (resid 51 through 63 )
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 86 )
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 105 )
12X-RAY DIFFRACTION12chain 'B' and (resid 106 through 110 )
13X-RAY DIFFRACTION13chain 'C' and (resid 9 through 68 )
14X-RAY DIFFRACTION14chain 'C' and (resid 69 through 127 )
15X-RAY DIFFRACTION15chain 'C' and (resid 128 through 183 )
16X-RAY DIFFRACTION16chain 'C' and (resid 184 through 221 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 7 )
18X-RAY DIFFRACTION18chain 'D' and (resid 8 through 17 )
19X-RAY DIFFRACTION19chain 'D' and (resid 18 through 44 )
20X-RAY DIFFRACTION20chain 'D' and (resid 45 through 51 )
21X-RAY DIFFRACTION21chain 'D' and (resid 52 through 64 )
22X-RAY DIFFRACTION22chain 'D' and (resid 65 through 73 )
23X-RAY DIFFRACTION23chain 'D' and (resid 74 through 83 )
24X-RAY DIFFRACTION24chain 'D' and (resid 84 through 91 )
25X-RAY DIFFRACTION25chain 'D' and (resid 92 through 108 )
26X-RAY DIFFRACTION26chain 'D' and (resid 109 through 119 )
27X-RAY DIFFRACTION27chain 'E' and (resid 0 through 8 )
28X-RAY DIFFRACTION28chain 'E' and (resid 9 through 17 )
29X-RAY DIFFRACTION29chain 'E' and (resid 18 through 40 )
30X-RAY DIFFRACTION30chain 'E' and (resid 41 through 50 )
31X-RAY DIFFRACTION31chain 'E' and (resid 51 through 69 )
32X-RAY DIFFRACTION32chain 'E' and (resid 70 through 86 )
33X-RAY DIFFRACTION33chain 'E' and (resid 87 through 105 )
34X-RAY DIFFRACTION34chain 'E' and (resid 106 through 110 )
35X-RAY DIFFRACTION35chain 'F' and (resid 9 through 64 )
36X-RAY DIFFRACTION36chain 'F' and (resid 65 through 84 )
37X-RAY DIFFRACTION37chain 'F' and (resid 85 through 141 )
38X-RAY DIFFRACTION38chain 'F' and (resid 142 through 174 )
39X-RAY DIFFRACTION39chain 'F' and (resid 175 through 190 )
40X-RAY DIFFRACTION40chain 'F' and (resid 191 through 221 )
41X-RAY DIFFRACTION41chain 'G' and (resid 1 through 7 )
42X-RAY DIFFRACTION42chain 'G' and (resid 8 through 17 )
43X-RAY DIFFRACTION43chain 'G' and (resid 18 through 51 )
44X-RAY DIFFRACTION44chain 'G' and (resid 52 through 64 )
45X-RAY DIFFRACTION45chain 'G' and (resid 65 through 83 )
46X-RAY DIFFRACTION46chain 'G' and (resid 84 through 118 )
47X-RAY DIFFRACTION47chain 'H' and (resid 0 through 8 )
48X-RAY DIFFRACTION48chain 'H' and (resid 9 through 17 )
49X-RAY DIFFRACTION49chain 'H' and (resid 18 through 110 )
50X-RAY DIFFRACTION50chain 'I' and (resid 10 through 122 )
51X-RAY DIFFRACTION51chain 'I' and (resid 123 through 183 )
52X-RAY DIFFRACTION52chain 'I' and (resid 184 through 219 )

+
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