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- PDB-6gy4: Crystal structure of the N-terminal KH domain of human BICC1 -

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Basic information

Entry
Database: PDB / ID: 6gy4
TitleCrystal structure of the N-terminal KH domain of human BICC1
ComponentsProtein bicaudal C homolog 1
KeywordsRNA BINDING PROTEIN / Bicaudal / RNA binding / Transcription / KH domain
Function / homology
Function and homology information


determination of left/right symmetry / kidney development / negative regulation of canonical Wnt signaling pathway / heart development / RNA binding / cytoplasm
Similarity search - Function
BICC1, SAM domain / : / : / : / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / SAM domain (Sterile alpha motif) / K Homology domain, type 1 superfamily / SAM domain profile. ...BICC1, SAM domain / : / : / : / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / SAM domain (Sterile alpha motif) / K Homology domain, type 1 superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
Protein bicaudal C homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.986 Å
AuthorsNewman, J.A. / Katis, V.L. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the N-terminal KH domain of human BICC1
Authors: Newman, J.A. / Katis, V.L. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionJun 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein bicaudal C homolog 1
B: Protein bicaudal C homolog 1
C: Protein bicaudal C homolog 1
D: Protein bicaudal C homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8359
Polymers39,0534
Non-polymers7825
Water64936
1
A: Protein bicaudal C homolog 1


Theoretical massNumber of molelcules
Total (without water)9,7631
Polymers9,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein bicaudal C homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8592
Polymers9,7631
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein bicaudal C homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4495
Polymers9,7631
Non-polymers6864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein bicaudal C homolog 1


Theoretical massNumber of molelcules
Total (without water)9,7631
Polymers9,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.406, 153.164, 86.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-203-

XPE

21B-311-

HOH

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Components

#1: Protein
Protein bicaudal C homolog 1 / Bic-C


Mass: 9763.319 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BICC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H694
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.88 Å3/Da / Density % sol: 34.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Lithium Sulfate, 50 % PEG 400, 0.1 M acetate pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 1.986→19.74 Å / Num. obs: 11724 / % possible obs: 90.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.043 / Net I/σ(I): 10
Reflection shellResolution: 1.986→2.164 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 576 / CC1/2: 0.682 / Rpim(I) all: 0.457 / % possible all: 67.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zzk

1zzk


Resolution: 1.986→19.74 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3035 560 4.78 %
Rwork0.2557 --
obs0.2579 11716 56.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.986→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 47 36 2310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032297
X-RAY DIFFRACTIONf_angle_d0.5143060
X-RAY DIFFRACTIONf_dihedral_angle_d19.1761435
X-RAY DIFFRACTIONf_chiral_restr0.037342
X-RAY DIFFRACTIONf_plane_restr0.004388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9859-2.18550.364350.3556661X-RAY DIFFRACTION14
2.1855-2.50120.3831040.34951881X-RAY DIFFRACTION39
2.5012-3.14920.33481520.30573551X-RAY DIFFRACTION72
3.1492-19.74060.28642690.23045063X-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)
14.6577-5.6844-2.63577.98162.15112.8191-0.61470.6456-0.63170.9639-0.12370.25540.58890.09140.67830.6210.0765-0.11250.3392-0.03460.35896.062558.274351.1356
29.29352.1415-1.58967.4008-0.69888.8144-0.44860.07010.7771-1.0888-0.26441.1801-0.4707-0.16790.54940.55720.1124-0.20640.4472-0.10730.413-6.196971.192249.7264
33.718-2.894-2.63082.43812.27742.18490.35080.14971.7736-2.631.2649-1.6003-0.52830.0622-2.04410.9241-0.18850.17560.6250.04691.03652.280378.84348.7648
48.92940.20.80862.01672.36058.97521.2105-0.1610.6821-0.41131.1644-2.0636-0.1126-0.4596-0.88830.54920.02120.23950.390.01740.925311.388671.337651.55
55.52691.6092-0.45161.56091.10621.46770.60170.95551.5208-0.85550.91730.7234-0.6741-1.8471.67430.67060.1140.10390.8880.52070.79084.069964.770746.4276
63.3614-4.462-0.18526.7462-1.575.47350.71260.5046-1.28140.02330.0375-0.4193-0.14820.0433-0.4410.41880.1679-0.02980.3923-0.06470.67727.200460.049750.0545
76.16560.3927-7.56393.5827-0.98789.32310.5597-2.2591.16111.2126-0.8501-1.6298-1.02510.8332-0.02310.37750.0299-0.15850.4484-0.06640.758311.111362.839257.9338
85.3129-0.688-0.66490.9154-1.47569.1889-0.1368-0.8893-1.37050.95440.3112-0.7856-0.4156-0.2788-0.21940.63020.13470.00960.3382-0.05410.7105-0.165865.985357.8594
94.8043.1335-0.24272.61251.10733.09230.42620.0109-0.2396-0.0748-0.5159-0.71480.31290.4235-0.04990.23570.00440.00810.43960.08420.455818.26452.694429.1116
107.7012-3.10284.73563.2998-1.79455.84990.33660.0041-0.5429-0.3165-0.43531.3367-0.5522-0.503-0.05990.377-0.11720.00990.39460.05810.5263.916742.205727.3986
114.0473-3.98872.94363.9253-2.8772.1370.12420.625-1.7375-0.45240.33172.14580.1667-0.7336-0.31260.5865-0.192-0.20910.689-0.12650.9375-2.550952.141227.4581
123.2972.497-5.42965.5409-1.93542.04810.24480.31321.68110.1904-0.14050.9003-0.1654-1.61510.04430.34550.0486-0.01770.4393-0.21541.02864.801658.849629.4502
137.7867-5.0616-0.24849.25582.11165.3450.74431.1695-0.3119-0.7378-1.41350.75920.1017-0.46120.50630.3531-0.06220.04110.4051-0.01770.427410.970749.103621.9464
146.1293-0.3165-1.59961.81521.94717.1819-0.01260.2385-0.42930.3582-0.2631-1.27691.1320.1103-0.03590.5282-0.02470.01510.2491-0.02550.642117.310347.572425.8776
152.48080.4819-0.70287.4397-5.06723.5823-0.0007-0.82420.47290.5579-0.224-0.5533-0.7492-1.063-0.09370.4257-0.00650.00820.4067-0.08720.415313.625860.372834.9723
164.4399-4.58295.13534.7314-5.29425.99360.04470.4311-0.75332.2968-0.3481-0.2922-1.85831.49960.47220.5116-0.1394-0.07420.58010.05130.678212.877146.170336.6724
175.00413.01-2.19162.1277-1.1224.9192-0.46220.8765-0.0287-0.42531.7061-0.1162-0.11170.3204-0.9550.319-0.0211-0.03870.3331-0.06450.474825.400866.275629.1639
189.43210.5398-1.65188.99270.31618.6996-0.19010.12911.206-1.05440.2915-0.8563-0.23891.2129-0.17940.6061-0.20730.1060.4514-0.02540.377639.28879.356727.1819
195.5186-4.08095.54763.0265-4.1195.59180.86870.94750.7243-1.0131-0.7332-0.91140.04621.703-0.86170.63840.02580.11740.7044-0.15791.10241.190568.829927.2128
204.24342.04772.85684.3048-1.6054.55770.59210.5801-0.57730.1104-0.3358-2.32180.16451.6662-0.36170.4072-0.0033-0.03410.3389-0.01130.759236.887361.069329.3286
212.74292.2719-0.20963.0408-1.93562.68261.06540.88210.72210.6666-1.00940.5107-1.12960.06550.08570.62030.05330.07480.39230.07020.640132.760376.377519.9506
229.3849-0.15720.01339.13010.2717.44740.5858-0.0445-0.50680.70480.0046-0.2048-0.4168-0.1244-0.30970.19370.00530.08280.21870.01430.385127.91664.564529.8381
232.03121.9242-3.01315.40952.51952.17560.1841-1.3526-3.2142.1556-0.7437-0.5515-0.5505-0.1426-0.29190.1588-0.5715-1.17640.2809-0.4416-1.174631.543965.844536.46
244.0869-3.05282.3287.96990.50572.2365-0.8737-0.607-0.16741.1349-0.09860.09850.1717-1.27680.09940.4312-0.12520.06090.5334-0.20370.635730.888675.613735.9529
254.4422-5.6974-0.33256.96230.25282.1121-0.6296-0.02470.44780.53890.10790.2257-0.16060.46120.19590.41190.0877-0.0430.24420.04330.588918.19748.692550.9699
266.30.11370.96075.280.66483.07540.02220.5278-0.2727-0.7823-0.0925-0.2907-0.8647-0.3389-0.09040.43210.13430.00260.45480.02980.379626.618635.465149.1505
273.269-3.452-1.68385.3666-1.58137.3157-0.53641.0306-0.91620.5237-0.2476-0.35830.5446-1.58680.77940.65670.08040.08060.6488-0.29160.739820.269629.569949.3175
282.152-2.7743-2.61798.8677-0.02929.6553-0.2590.1567-0.9913-0.46490.25150.2917-0.1084-0.85340.24680.4439-0.0113-0.14840.36460.01730.625310.705836.91351.6996
294.4669-0.2597-2.08886.305-4.2155.89620.3792.2924-1.7561-1.0732-1.2671-0.5415-0.44460.54670.09050.69560.1974-0.07970.7586-0.11210.541518.518443.491144.8557
309.35250.1207-1.89034.8915-0.54435.4652-0.38630.881-0.0482-0.2617-0.0528-0.01760.67230.1157-0.22690.37310.088-0.14140.38820.13070.442414.40747.985151.735
314.7713-5.8135-0.76657.10641.21753.26180.08580.0858-1.17423.4717-0.01951.44321.625-0.9534-0.24970.60520.0773-0.06070.2514-0.01470.485714.16344.396758.0526
324.38215.13820.5388.7188-4.19638.731.68380.3514-0.37971.54-0.474-0.4707-2.4521-0.807-0.99320.58770.04730.06870.406-0.03540.425624.536943.233657.892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 45:54)
2X-RAY DIFFRACTION2(chain A and resid 55:63)
3X-RAY DIFFRACTION3(chain A and resid 64:76)
4X-RAY DIFFRACTION4(chain A and resid 77:85)
5X-RAY DIFFRACTION5(chain A and resid 86:103)
6X-RAY DIFFRACTION6(chain A and resid 104:112)
7X-RAY DIFFRACTION7(chain A and resid 113:120)
8X-RAY DIFFRACTION8(chain A and resid 121:128)
9X-RAY DIFFRACTION9(chain B and resid 45:55)
10X-RAY DIFFRACTION10(chain B and resid 56:68)
11X-RAY DIFFRACTION11(chain B and resid 69:76)
12X-RAY DIFFRACTION12(chain B and resid 77:85)
13X-RAY DIFFRACTION13(chain B and resid 86:97)
14X-RAY DIFFRACTION14(chain B and resid 98:108)
15X-RAY DIFFRACTION15(chain B and resid 109:121)
16X-RAY DIFFRACTION16(chain B and resid 122:130)
17X-RAY DIFFRACTION17(chain C and resid 45:54)
18X-RAY DIFFRACTION18(chain C and resid 55:68)
19X-RAY DIFFRACTION19(chain C and resid 74:78)
20X-RAY DIFFRACTION20(chain C and resid 79:88)
21X-RAY DIFFRACTION21(chain C and resid 89:98)
22X-RAY DIFFRACTION22(chain C and resid 103:115)
23X-RAY DIFFRACTION23(chain C and resid 116:122)
24X-RAY DIFFRACTION24(chain C and resid 123:128)
25X-RAY DIFFRACTION25(chain D and resid 45:56)
26X-RAY DIFFRACTION26(chain D and resid 57:64)
27X-RAY DIFFRACTION27(chain D and resid 65:76)
28X-RAY DIFFRACTION28(chain D and resid 77:85)
29X-RAY DIFFRACTION29(chain D and resid 86:102)
30X-RAY DIFFRACTION30(chain D and resid 103:114)
31X-RAY DIFFRACTION31(chain D and resid 115:122)
32X-RAY DIFFRACTION32(chain D and resid 123:128)

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