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- PDB-4e4s: Crystal structure of Pika GITRL -

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Basic information

Entry
Database: PDB / ID: 4e4s
TitleCrystal structure of Pika GITRL
ComponentsTumor necrosis factor ligand superfamily member 18
KeywordsIMMUNE SYSTEM / GITRL / GLUCOCORTICOID-INDUCED TNF RECEPTOR LIGAND / TNFRSF18 / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / IFN / Atoms-to-Animals: The Immune Function Network
Function / homologyJelly Rolls - #40 / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesOchotona princeps (American pika)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKumar, P.R. / Bhosle, R. / Bonanno, J. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hillerich, B. / Hammonds, J. / Seidel, R. / Toro, R. ...Kumar, P.R. / Bhosle, R. / Bonanno, J. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hillerich, B. / Hammonds, J. / Seidel, R. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of GITRL from Ochotona princeps
Authors: Kumar, P.R. / Bhosle, R. / Bonanno, J. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hillerich, B. / Hammonds, J. / Seidel, R. / Toro, R. / Nathenson, S.G. / Almo, S.C.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 18
B: Tumor necrosis factor ligand superfamily member 18
C: Tumor necrosis factor ligand superfamily member 18
D: Tumor necrosis factor ligand superfamily member 18
E: Tumor necrosis factor ligand superfamily member 18
F: Tumor necrosis factor ligand superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,64015
Polymers83,8796
Non-polymers7619
Water4,342241
1
A: Tumor necrosis factor ligand superfamily member 18
B: Tumor necrosis factor ligand superfamily member 18
F: Tumor necrosis factor ligand superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2407
Polymers41,9393
Non-polymers3014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tumor necrosis factor ligand superfamily member 18
D: Tumor necrosis factor ligand superfamily member 18
E: Tumor necrosis factor ligand superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4008
Polymers41,9393
Non-polymers4605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.371, 164.588, 54.103
Angle α, β, γ (deg.)90.000, 117.160, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer. Two such trimers are present in the asymmetric unit (Chains A-C and chains D-F)

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Components

#1: Protein
Tumor necrosis factor ligand superfamily member 18


Mass: 13979.791 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: synthesized gene / Source: (gene. exp.) Ochotona princeps (American pika) / Strain: synthetic geneArtificial gene synthesis / Gene: GITRL / Plasmid: modified pET28b with N-terminal Smt3 tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2 M Calcium Chloride, 0.1 M HEPES:NaOH pH 7.5, 30% (w/v) PEG 4000); Cryoprotection (30% glycerol), Sitting Drop Vapor ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2 M Calcium Chloride, 0.1 M HEPES:NaOH pH 7.5, 30% (w/v) PEG 4000); Cryoprotection (30% glycerol), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.441
ReflectionResolution: 1.95→50 Å / Num. obs: 55662 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.094 / Χ2: 0.962 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.987.40.75527450.8871100
1.98-2.027.50.62927710.9021100
2.02-2.067.50.55128280.941100
2.06-2.17.50.46527480.9591100
2.1-2.157.60.39228020.9551100
2.15-2.27.60.35827460.9631100
2.2-2.257.60.29428300.9561100
2.25-2.317.60.27827100.9871100
2.31-2.387.60.2427940.9971100
2.38-2.467.60.21628490.9871100
2.46-2.547.60.18127190.9691100
2.54-2.657.60.16427520.9931100
2.65-2.777.60.13627880.9981100
2.77-2.917.60.1127860.991100
2.91-3.17.60.09527791.0551100
3.1-3.337.50.07728031.0971100
3.33-3.677.40.06227881.0531100
3.67-4.27.30.05327970.9491100
4.2-5.297.20.04727910.831100
5.29-507.40.04628360.757199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.203 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.7765 / σ(F): 1.36 / Phase error: 29.85 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 2616 5.14 %RANDOM
Rwork0.1467 ---
obs0.1483 50869 91.35 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.01 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 119.17 Å2 / Biso mean: 26.2909 Å2 / Biso min: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.2223 Å20 Å20.1262 Å2
2--0.8726 Å2-0 Å2
3---1.3496 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 49 241 5732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065625
X-RAY DIFFRACTIONf_angle_d1.0947597
X-RAY DIFFRACTIONf_chiral_restr0.072827
X-RAY DIFFRACTIONf_plane_restr0.004975
X-RAY DIFFRACTIONf_dihedral_angle_d13.9362077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9505-1.9880.2431730.18441570164351
1.988-2.02860.2289940.1761836193060
2.0286-2.07270.21761050.1782080218567
2.0727-2.12090.16771370.18042265240274
2.1209-2.17390.2131170.16172554267182
2.1739-2.23270.22071460.16812740288689
2.2327-2.29840.21891340.17292895302994
2.2984-2.37260.1971640.16032969313395
2.3726-2.45740.1951550.16542989314495
2.4574-2.55580.21251340.1642903303796
2.5558-2.67210.17821480.16142922307095
2.6721-2.81290.19921590.16942940309995
2.8129-2.98910.17251730.15092928310194
2.9891-3.21990.19861660.15152928309495
3.2199-3.54380.16221700.12782928309895
3.5438-4.05620.1471670.11562943311095
4.0562-5.10920.14051660.10422929309595
5.1092-43.93980.18011790.16332961314094
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)
10.44940.2347-0.13850.4198-0.26251.6257-0.08490.0175-0.02420.21970.1210.1835-0.009-0.1289-0.23670.27210.02960.18310.0770.10930.0714-25.0904-22.362866.0495
21.31820.6635-0.65921.61-1.13491.4646-0.15190.0592-0.12870.10080.09010.13190.2148-0.1231-0.00010.20390.00420.1370.05240.00750.1047-20.6357-32.060563.888
31.8357-0.31922.65032.44520.25636.7227-0.0957-0.02110.10350.1890.0642-0.207-0.42280.49430.03310.1594-0.0685-0.04140.14670.00920.0253-3.9074-16.713853.2278
43.60090.2624-2.41590.0191-0.17591.6209-0.0064-0.55750.06960.53240.00860.1309-0.41170.3710.01470.3284-0.00080.03960.1550.0290.0864-9.7442-27.046767.5762
51.04740.403-0.43281.0324-0.68412.4104-0.0537-0.0747-0.0340.2101-0.09150.0004-0.10310.1778-0.01680.27510.01480.08240.09020.02360.0406-13.3551-29.301963.8766
60.1446-0.28530.28660.7908-0.85191.1816-0.04260.03290.06950.24260.10830.1728-0.1818-0.1218-0.13110.2408-0.01820.07670.09010.03750.045-17.4465-24.183760.4066
71.62520.2780.88163.52411.65443.38290.1212-0.3291-0.21970.2771-0.06790.14930.193-0.1695-0.02540.12820.00040.0290.10070.03490.0816-20.6902-52.363274.7374
84.48980.881.78732.35760.72183.45050.11170.2219-0.2207-0.0193-0.0049-0.6579-0.04480.7812-0.04120.1867-0.02040.08940.25070.07220.2344-6.5101-47.990868.5415
90.11350.07690.21640.20.28960.551-0.02710.12680.1395-0.1707-0.0921-0.5192-0.19780.5672-0.110.2296-0.05240.09850.35820.16430.4258-3.0895-40.289367.589
102.48592.62771.15043.9559-0.20473.0432-0.03890.3036-0.1546-0.2470.1512-0.0520.26610.3142-0.06140.16550.04380.08790.11880.01850.0895-16.0822-52.59563.6095
115.54141.58653.02041.72411.11985.00830.317-0.296-0.36220.0785-0.1462-0.3703-0.00590.2074-0.11510.1683-0.01740.04210.13090.08830.1572-11.793-47.061272.3125
121.26310.4533-0.28391.3102-1.12380.99530.106-0.37010.23260.2959-0.1756-0.0073-0.23720.26290.04280.21840.0047-0.0730.1809-0.0670.1251-29.8994-70.860377.8941
131.26480.12120.10312.1883-0.43921.4234-0.0055-0.1191-0.04720.08260.05250.5790.029-0.5619-0.0190.118-0.0003-0.03180.2495-0.0640.191-43.7585-77.619874.2871
142.84383.5902-0.9964.5472-1.0343.661-0.11130.15990.3876-0.24390.10110.5484-0.1908-0.48570.0650.19410.0311-0.1360.1744-0.04640.2015-41.6075-70.481466.36
154.01350.55041.19653.58130.11733.6727-0.16630.2865-0.6413-0.1792-0.02470.96420.747-0.89670.18830.3555-0.1098-0.05430.2925-0.05760.3703-46.2154-83.223970.6955
163.33972.3293-1.47713.8526-0.79743.58290.17860.08280.2087-0.1953-0.2310.0439-0.3531-0.12710.01290.15850.0332-0.08480.0657-0.00860.073-33.2945-70.616966.5198
173.14510.8866-2.61711.4193-1.4014.27190.0539-0.193-0.054-0.0763-0.08880.3367-0.0559-0.08350.090.14590.0164-0.02980.0674-0.07880.2025-36.6042-75.839774.5677
185.3839-2.17340.56275.7721-0.08683.37690.07440.34280.1891-0.1-0.149-0.6596-0.1620.61740.06770.1903-0.0218-0.02120.19980.00970.1332-21.8096-77.422747.0864
192.2852-0.10691.53390.1155-0.03661.80950.01320.0783-0.0277-0.0235-0.05290.01420.0489-0.0542-0.01880.24960.0171-0.11210.1016-0.02660.0757-36.2769-81.528748.0289
206.59052.58057.14883.54222.11568.8139-0.1607-0.98240.12030.4565-0.12310.3676-0.1119-1.04230.23750.17690.0261-0.02970.2951-0.00230.1826-42.5188-77.822553.5639
212.6444-1.6367-1.00914.4390.0892.95290.08820.0409-0.1395-0.25590.0439-0.27670.33570.272-0.0740.21080.0284-0.04190.0431-0.04070.127-27.0949-87.263750.6751
220.6528-0.10310.45651.6377-0.3241.4013-0.14810.19530.15630.1174-0.0711-0.1096-0.03930.0696-0.05270.23770.0089-0.10110.1333-0.05340.0996-31.2732-77.284949.3776
230.11040.1057-0.42580.275-0.30921.7008-0.0243-0.0980.04290.29420.0819-0.2915-0.02980.2275-0.17590.33560.0596-0.18210.0878-0.10510.1704-22.4507-99.495469.2678
241.52230.63222.26641.27081.75974.6467-0.0451-0.11540.11270.28910.0724-0.21480.04320.0395-0.12390.21750.0255-0.11880.056-0.02890.1031-26.9276-89.640869.9834
250.2691-0.19140.8173.58682.91836.03290.03350.11-0.12140.217-0.04090.08950.4157-0.4535-0.03020.1596-0.01520.01050.1188-0.04180.0067-43.6646-105.070656.2957
262.0104-0.3831.75750.6718-0.29821.5387-0.0076-0.5365-0.02830.5656-0.0090.00820.0684-0.67440.03390.3259-0.00940.04250.1744-0.00170.0529-39.6513-96.286871.2807
270.51790.2937-0.1740.81740.47511.0303-0.09020.00040.05980.1569-0.0002-0.0403-0.0241-0.1447-0.0490.29430.0566-0.07330.1164-0.02920.0554-36.4507-91.922265.0346
283.025-1.12772.66892.34692.47068.58910.1727-0.38-0.06650.5003-0.34210.24460.76-0.58050.15090.3556-0.0444-0.02780.1332-0.01620.1019-34.3722-99.710472.3232
290.1944-0.08330.08530.38580.53441.2119-0.04760.00270.00360.1860.1317-0.13510.03870.09530.03590.24170.0409-0.07470.0529-0.08720.0665-31.3466-98.225164.3081
302.6972-1.3326-0.23724.3273-0.37142.9658-0.01310.2478-0.5368-0.2704-0.07950.57660.2211-0.53320.06830.2231-0.07680.00240.2124-0.03110.1865-27.6116-45.772244.0767
311.9580.0962-1.42640.03450.03821.46990.0383-0.00960.1107-0.0964-0.077-0.1114-0.09610.1007-0.040.23070.01850.06830.09610.05630.063-13.1644-41.721644.9794
325.28140.3348-0.14952.52-0.55540.1524-0.2999-0.1827-0.16320.09880.1278-0.2033-0.03980.31750.16230.3048-0.01220.04170.25350.0150.1104-6.8981-45.528150.3956
334.2795-2.16682.56044.829-0.0282.1098-0.07950.02130.1348-0.1643-0.00950.0921-0.5724-0.26670.01390.23720.03550.03820.12510.05790.0921-22.3641-36.03247.6577
342.5992-1.9912-1.1984.00341.33060.7256-0.19550.2315-0.34620.0436-0.05180.18440.2285-0.22620.24890.16480.02710.01360.15570.03520.0827-19.8534-43.948947.6531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:39)A4 - 39
2X-RAY DIFFRACTION2chain 'A' and (resseq 40:49)A40 - 49
3X-RAY DIFFRACTION3chain 'A' and (resseq 50:61)A50 - 61
4X-RAY DIFFRACTION4chain 'A' and (resseq 62:74)A62 - 74
5X-RAY DIFFRACTION5chain 'A' and (resseq 75:99)A75 - 99
6X-RAY DIFFRACTION6chain 'A' and (resseq 100:121)A100 - 121
7X-RAY DIFFRACTION7chain 'B' and (resseq 4:39)B4 - 39
8X-RAY DIFFRACTION8chain 'B' and (resseq 40:74)B40 - 74
9X-RAY DIFFRACTION9chain 'B' and (resseq 75:84)B75 - 84
10X-RAY DIFFRACTION10chain 'B' and (resseq 85:99)B85 - 99
11X-RAY DIFFRACTION11chain 'B' and (resseq 100:121)B100 - 121
12X-RAY DIFFRACTION12chain 'C' and (resseq 4:39)C4 - 39
13X-RAY DIFFRACTION13chain 'C' and (resseq 40:61)C40 - 61
14X-RAY DIFFRACTION14chain 'C' and (resseq 62:74)C62 - 74
15X-RAY DIFFRACTION15chain 'C' and (resseq 75:84)C75 - 84
16X-RAY DIFFRACTION16chain 'C' and (resseq 85:99)C85 - 99
17X-RAY DIFFRACTION17chain 'C' and (resseq 100:123)C100 - 123
18X-RAY DIFFRACTION18chain 'D' and (resseq 3:39)D3 - 39
19X-RAY DIFFRACTION19chain 'D' and (resseq 40:74)D40 - 74
20X-RAY DIFFRACTION20chain 'D' and (resseq 75:84)D75 - 84
21X-RAY DIFFRACTION21chain 'D' and (resseq 85:99)D85 - 99
22X-RAY DIFFRACTION22chain 'D' and (resseq 100:123)D100 - 123
23X-RAY DIFFRACTION23chain 'E' and (resseq 3:39)E3 - 39
24X-RAY DIFFRACTION24chain 'E' and (resseq 40:47)E40 - 47
25X-RAY DIFFRACTION25chain 'E' and (resseq 48:61)E48 - 61
26X-RAY DIFFRACTION26chain 'E' and (resseq 62:74)E62 - 74
27X-RAY DIFFRACTION27chain 'E' and (resseq 75:93)E75 - 93
28X-RAY DIFFRACTION28chain 'E' and (resseq 94:99)E94 - 99
29X-RAY DIFFRACTION29chain 'E' and (resseq 100:123)E100 - 123
30X-RAY DIFFRACTION30chain 'F' and (resseq 3:39)F3 - 39
31X-RAY DIFFRACTION31chain 'F' and (resseq 40:74)F40 - 74
32X-RAY DIFFRACTION32chain 'F' and (resseq 75:84)F75 - 84
33X-RAY DIFFRACTION33chain 'F' and (resseq 85:99)F85 - 99
34X-RAY DIFFRACTION34chain 'F' and (resseq 100:124)F100 - 124

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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

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