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- PDB-7tlh: Murine meteorin C-terminal NTR domain -

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Basic information

Entry
Database: PDB / ID: 7tlh
TitleMurine meteorin C-terminal NTR domain
ComponentsMeteorin
KeywordsSIGNALING PROTEIN / meteorin / NTR / neurotrophic factor
Function / homologyMeteorin / radial glial cell differentiation / glial cell differentiation / positive regulation of axonogenesis / axonogenesis / hormone activity / extracellular space / Meteorin
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsQuan, C. / Arndt, J.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Identification and structure determination of stable domains of meteorin and meteorin-like
Authors: Quan, C. / Arndt, J.W. / Gong, B.J. / Dolnikova, J. / Pepinsky, R.B.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Meteorin
C: Meteorin
A: Meteorin
D: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,18310
Polymers58,6074
Non-polymers5766
Water5,368298
1
B: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7482
Polymers14,6521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8443
Polymers14,6521
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8443
Polymers14,6521
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7482
Polymers14,6521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.757, 75.672, 75.725
Angle α, β, γ (deg.)90.000, 128.500, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 147 through 157 or resid 159...
21(chain B and (resid 147 through 157 or resid 159...
31(chain C and (resid 147 through 157 or resid 159 through 178 or resid 180 through 270))
41(chain D and (resid 13 through 23 or resid 25...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 147 through 157 or resid 159...A147 - 157
121(chain A and (resid 147 through 157 or resid 159...A159 - 178
131(chain A and (resid 147 through 157 or resid 159...A180 - 200
141(chain A and (resid 147 through 157 or resid 159...A201
151(chain A and (resid 147 through 157 or resid 159...A147 - 270
161(chain A and (resid 147 through 157 or resid 159...A147 - 270
171(chain A and (resid 147 through 157 or resid 159...A147 - 270
181(chain A and (resid 147 through 157 or resid 159...A147 - 270
211(chain B and (resid 147 through 157 or resid 159...B147 - 157
221(chain B and (resid 147 through 157 or resid 159...B159 - 178
231(chain B and (resid 147 through 157 or resid 159...B180 - 200
241(chain B and (resid 147 through 157 or resid 159...B147 - 270
251(chain B and (resid 147 through 157 or resid 159...B147 - 270
261(chain B and (resid 147 through 157 or resid 159...B147 - 270
271(chain B and (resid 147 through 157 or resid 159...B147 - 270
281(chain B and (resid 147 through 157 or resid 159...B147 - 270
311(chain C and (resid 147 through 157 or resid 159 through 178 or resid 180 through 270))C147 - 157
321(chain C and (resid 147 through 157 or resid 159 through 178 or resid 180 through 270))C159 - 178
331(chain C and (resid 147 through 157 or resid 159 through 178 or resid 180 through 270))C180 - 270
411(chain D and (resid 13 through 23 or resid 25...D13 - 23
421(chain D and (resid 13 through 23 or resid 25...D25 - 44
431(chain D and (resid 13 through 23 or resid 25...D46 - 67
441(chain D and (resid 13 through 23 or resid 25...D74 - 136

NCS oper:
IDCodeMatrixVector
1given(0.61008532493, -0.628205404804, 0.482860089135), (0.616303534103, -0.0067569970697, -0.78747971202), (0.497961695472, 0.778018195395, 0.38304286637)-25.5670852058, 134.864524925, 2.15168141249
2given(0.599786099883, 0.651718964303, 0.464240267485), (-0.617824546376, 0.00850734344603, 0.786269963183), (0.508477594671, -0.758412827341, 0.407750559831)-72.7283803668, -59.4944696864, 58.4512011124
3given(0.235735799726, 0.00431559298754, 0.97180759844), (0.00126082661317, -0.999990656401, 0.00413490355586), (0.97181636282, 0.000250536086464, -0.235739038319)-73.1880135708, 75.1049267635, 92.7373886801

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Components

#1: Protein
Meteorin / Hypoxia/reoxygenation regulatory factor


Mass: 14651.735 Da / Num. of mol.: 4 / Fragment: NTR domain (UNP residues 156-291)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Metrn, Hyrac / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8C1Q4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris, pH 5.4, 1 M ammonium sulfate, 1% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.25 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. obs: 55117 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 22.78 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8027 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→19.99 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 2866 5.2 %
Rwork0.172 52231 -
obs0.1737 55097 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.56 Å2 / Biso mean: 34.3121 Å2 / Biso min: 15.06 Å2
Refinement stepCycle: final / Resolution: 1.74→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 30 298 4031
Biso mean--62.71 38.09 -
Num. residues----487
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2140X-RAY DIFFRACTION6.095TORSIONAL
12B2140X-RAY DIFFRACTION6.095TORSIONAL
13C2140X-RAY DIFFRACTION6.095TORSIONAL
14D2140X-RAY DIFFRACTION6.095TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.770.31611820.290225582740100
1.77-1.80.33061160.261226052721100
1.8-1.830.28871880.250825832771100
1.83-1.870.27471590.224925812740100
1.87-1.910.22651010.218526082709100
1.91-1.950.2631150.19926522767100
1.95-20.18581180.175626222740100
2-2.060.23591430.16626222765100
2.06-2.120.17691630.173425842747100
2.12-2.190.20071410.151425942735100
2.19-2.260.20231330.154126272760100
2.26-2.350.16221160.149626352751100
2.35-2.460.1751190.159526532772100
2.46-2.590.21011360.1625852721100
2.59-2.750.1751560.15626642820100
2.75-2.960.20391360.17426102746100
2.96-3.260.19561310.166126322763100
3.26-3.730.18441630.162126012764100
3.73-4.690.1571730.145426212794100
4.69-19.990.26081770.19412594277198
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)
10.07210.10230.06630.08110.08590.09590.3302-0.3032-0.15890.4048-0.3708-0.4317-0.3940.0745-0.00460.4437-0.1015-0.0450.2741-0.06040.3613-35.688454.697750.5742
20.10720.058-0.08830.12580.03610.1299-0.0418-0.25030.1902-0.06230.05260.13320.1758-0.16460.00010.3322-0.05760.0510.2562-0.05630.3706-44.305653.964442.7186
30.1459-0.0665-0.15681.1976-0.00690.07880.0601-0.0588-0.0744-0.02330.0521-0.13780.0834-0.140200.2373-0.05060.00990.22860.00040.2046-32.109669.583543.9588
40.09420.1645-0.050.3494-0.10390.0458-0.19290.3238-0.1939-0.7444-0.01470.24580.0749-0.5808-0.00880.3473-0.0751-0.080.37320.01350.3604-42.897162.460231.9383
50.08020.02530.36541.3480.21481.9517-0.47290.47830.8845-0.6742-0.18660.4165-0.838-0.5239-0.63610.6404-0.0278-0.18490.3830.06510.4665-39.693571.527831.0134
60.35110.32530.17260.31750.18470.1060.0631-0.00820.08940.0142-0.1181-0.2930.01450.08980.00470.2345-0.0484-0.0480.23830.00960.2501-33.275668.400346.7475
70.05870.0921-0.04890.1253-0.0770.0570.1601-0.2682-0.45070.16290.5697-0.80750.54490.2720.05560.33140.01370.09120.2968-0.07790.5765-24.281763.25642.3473
80.1286-0.0243-0.00230.1803-0.13310.0547-0.05970.2397-0.21990.1215-0.23090.44270.3122-0.28440.00010.2947-0.06060.02510.2616-0.0040.339-40.152464.7843.0078
90.36940.3760.03810.3470.33620.07590.04470.0574-0.002-0.1145-0.0508-0.1299-0.06550.0305-00.2697-0.04070.03420.2135-0.01280.2347-37.787953.76938.1895
100.1123-0.10770.10390.1398-0.0760.0468-0.14290.29390.0047-0.74490.00130.542-0.11320.1256-0.00590.3589-0.0331-0.02320.28770.01280.2739-46.433349.220633.2458
110.103-0.0570.00720.0444-0.02770.0022-0.27790.5010.10250.1546-0.2815-0.21180.04570.57280.00040.26710.03060.03040.28580.04580.2941-26.92620.799840.2478
120.6745-0.1472-0.39570.6422-0.00950.13060.1289-0.01050.0641-0.058-0.00130.128-0.0907-0.02980.00010.2311-0.00550.00850.21180.01180.2243-36.238614.685539.3909
130.18090.4020.05670.8690.30220.5277-0.11530.05650.0709-0.0160.0457-0.01450.1492-0.0368-0.00020.2135-0.0118-0.01770.24290.04490.2517-29.72433.690944.0097
141.3126-1.1824-0.81871.21350.25971.9522-0.20650.3898-0.4301-0.41510.15950.45190.319-0.3452-0.17120.2844-0.0795-0.09170.34950.01530.4343-45.21569.263635.9815
150.1685-0.23720.11030.3444-0.1610.12480.07910.15340.0490.25150.0153-0.0470.1445-0.00480.00010.2399-0.0145-0.00790.23270.02730.2386-30.25567.021542.9696
160.03610.0351-0.02360.0306-0.0261-0.0052-0.4832-0.21810.34571.15170.2024-0.0076-0.17150.1082-0.0010.5060.03390.04260.28190.0160.3227-33.893612.765652.1746
170.22610.02170.21180.1769-0.04680.21840.02350.06130.127-0.35860.0539-0.0986-0.17420.1734-00.3179-0.02890.00430.21810.01580.2535-34.710610.182635.9948
180.3627-0.1239-0.55770.5245-0.62920.81190.07970.0506-0.00210.1414-0.01150.233-0.105-0.04290.00010.1957-0.02050.00360.19080.0110.229-39.681122.107239.8385
190.1545-0.05970.15860.1408-0.05390.10080.1311-0.3881-0.1577-0.02680.22970.76880.0472-0.3905-0.00110.266-0.0414-0.02850.36630.07680.331-46.020625.188132.4954
200.2112-0.2774-0.20220.31940.18020.21050.1331-0.04160.22410.099-0.11340.05370.38520.2625-0.00040.2135-0.00160.04760.2863-0.04220.2739-37.778444.065572.4957
210.0676-0.0185-0.14370.0222-0.03910.25360.0364-0.11970.05550.02-0.0688-0.02090.10830.0178-00.20140.0018-0.00110.2204-0.02320.2193-26.910834.150164.6695
220.2684-0.2346-0.23420.3524-0.07550.6205-0.0216-0.27650.0973-0.2169-0.1145-0.0034-0.1008-0.0379-0.00040.20310.00050.00040.2287-0.04230.2114-20.625739.599663.8035
230.37130.1062-0.14920.0973-0.00670.0622-0.08460.1064-0.1914-0.5420.0677-0.2096-0.0151-0.1197-0.00020.293-0.03960.02190.2718-0.06390.2971-35.622932.393356.0401
240.8414-0.01110.06140.06090.03990.0402-0.2233-0.2638-0.22350.11240.0772-0.09830.34290.2467-0.00550.26620.03790.01710.2702-0.01620.2444-23.549836.920968.0272
250.3915-0.13770.12180.15480.0380.14950.2047-0.14310.33950.2016-0.060.1655-0.26590.0198-0.00020.23560.01510.03260.2482-0.03670.2817-31.780641.399663.8
260.5582-0.4601-0.21930.59050.12420.1654-0.27330.0182-0.20990.11750.15660.00540.1592-0.026100.18620.00780.01350.2235-0.02060.1961-39.469236.293171.7594
270.1275-0.11650.09630.07850.00140.2399-0.0150.4409-0.2938-0.19320.40270.12980.1499-0.47040.00860.2498-0.0170.01670.3459-0.0270.2796-49.91738.093369.3602
280.2393-0.2299-0.19010.33410.32440.30020.0079-0.3965-0.00680.0509-0.0344-0.02550.28790.240900.27850.0280.00940.28270.00210.1947-11.377931.356238.9761
290.66590.015-0.27340.16020.17530.5561-0.0112-0.04570.03280.04790.0519-0.0529-0.00220.1468-0.00010.20530.0143-0.01940.1798-0.03030.1902-16.161238.572554.4173
300.19650.0153-0.04270.0042-0.00430.06920.07010.2570.2666-0.1271-0.04770.5035-0.1377-0.2112-00.23540.0129-0.01290.1942-0.01660.233-24.051740.912139.3106
310.25820.0114-0.28-0.0004-0.00830.3492-0.0372-0.09180.29640.1461-0.04250.524-0.3851-0.69560.0480.33680.08250.01740.3097-0.01720.3275-27.714141.570246.4672
320.06180.217-0.04170.3945-0.06960.62450.1759-0.28640.0422-0.3117-0.0063-0.1819-0.02640.48640.00040.2290.00220.00160.3197-0.04860.2179-12.436838.506353.8779
330.5095-0.07830.1840.1083-0.07210.1568-0.1773-0.091-0.2078-0.047-0.0527-0.27720.3080.2266-0.00140.241-0.01020.01250.2595-0.04320.221-18.57333.944746.765
340.34-0.1524-0.2070.290.04650.76690.06560.00620.0870.0020.0064-0.0266-0.15240.005600.2124-0.0110.00050.1923-0.01450.1852-14.232938.42534.3135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 147 through 152 )B147 - 152
2X-RAY DIFFRACTION2chain 'B' and (resid 153 through 164 )B153 - 164
3X-RAY DIFFRACTION3chain 'B' and (resid 165 through 189 )B165 - 189
4X-RAY DIFFRACTION4chain 'B' and (resid 190 through 195 )B190 - 195
5X-RAY DIFFRACTION5chain 'B' and (resid 196 through 209 )B196 - 209
6X-RAY DIFFRACTION6chain 'B' and (resid 210 through 219 )B210 - 219
7X-RAY DIFFRACTION7chain 'B' and (resid 220 through 226 )B220 - 226
8X-RAY DIFFRACTION8chain 'B' and (resid 227 through 237 )B227 - 237
9X-RAY DIFFRACTION9chain 'B' and (resid 238 through 259 )B238 - 259
10X-RAY DIFFRACTION10chain 'B' and (resid 260 through 270 )B260 - 270
11X-RAY DIFFRACTION11chain 'C' and (resid 147 through 152 )C147 - 152
12X-RAY DIFFRACTION12chain 'C' and (resid 153 through 177 )C153 - 177
13X-RAY DIFFRACTION13chain 'C' and (resid 178 through 189 )C178 - 189
14X-RAY DIFFRACTION14chain 'C' and (resid 190 through 209 )C190 - 209
15X-RAY DIFFRACTION15chain 'C' and (resid 210 through 219 )C210 - 219
16X-RAY DIFFRACTION16chain 'C' and (resid 220 through 227 )C220 - 227
17X-RAY DIFFRACTION17chain 'C' and (resid 228 through 237 )C228 - 237
18X-RAY DIFFRACTION18chain 'C' and (resid 238 through 260 )C238 - 260
19X-RAY DIFFRACTION19chain 'C' and (resid 261 through 270 )C261 - 270
20X-RAY DIFFRACTION20chain 'A' and (resid 147 through 164 )A147 - 164
21X-RAY DIFFRACTION21chain 'A' and (resid 165 through 177 )A165 - 177
22X-RAY DIFFRACTION22chain 'A' and (resid 178 through 189 )A178 - 189
23X-RAY DIFFRACTION23chain 'A' and (resid 190 through 209 )A190 - 209
24X-RAY DIFFRACTION24chain 'A' and (resid 210 through 226 )A210 - 226
25X-RAY DIFFRACTION25chain 'A' and (resid 227 through 237 )A227 - 237
26X-RAY DIFFRACTION26chain 'A' and (resid 238 through 259 )A238 - 259
27X-RAY DIFFRACTION27chain 'A' and (resid 260 through 270 )A260 - 270
28X-RAY DIFFRACTION28chain 'D' and (resid 13 through 30 )D13 - 30
29X-RAY DIFFRACTION29chain 'D' and (resid 31 through 55 )D31 - 55
30X-RAY DIFFRACTION30chain 'D' and (resid 56 through 61 )D56 - 61
31X-RAY DIFFRACTION31chain 'D' and (resid 62 through 75 )D62 - 75
32X-RAY DIFFRACTION32chain 'D' and (resid 76 through 92 )D76 - 92
33X-RAY DIFFRACTION33chain 'D' and (resid 93 through 103 )D93 - 103
34X-RAY DIFFRACTION34chain 'D' and (resid 104 through 136 )D104 - 136

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Yorodumi

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  • 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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