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- PDB-6y2d: Crystal structure of the second KH domain of FUBP1 -

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Basic information

Entry
Database: PDB / ID: 6y2d
TitleCrystal structure of the second KH domain of FUBP1
ComponentsFar upstream element-binding protein 1
KeywordsRNA BINDING PROTEIN / ssDNA/RNA binding motif
Function / homology
Function and homology information


single-stranded DNA binding / regulation of gene expression / mRNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 ...: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Far upstream element-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNi, X. / Chaikuad, A. / Joerger, A.C. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Sci Rep / Year: 2020
Title: Comparative structural analyses and nucleotide-binding characterization of the four KH domains of FUBP1.
Authors: Ni, X. / Knapp, S. / Chaikuad, A.
History
DepositionFeb 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Far upstream element-binding protein 1
B: Far upstream element-binding protein 1
C: Far upstream element-binding protein 1
D: Far upstream element-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7999
Polymers33,3234
Non-polymers4765
Water1,802100
1
A: Far upstream element-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5233
Polymers8,3311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Far upstream element-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5193
Polymers8,3311
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Far upstream element-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4272
Polymers8,3311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Far upstream element-binding protein 1


Theoretical massNumber of molelcules
Total (without water)8,3311
Polymers8,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.888, 82.181, 49.371
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARGAA184 - 2562 - 74
21METMETARGARGBB184 - 2562 - 74
12ASNASNASPASPAA185 - 2573 - 75
22ASNASNASPASPCC185 - 2573 - 75
13SERSERARGARGAA183 - 2561 - 74
23SERSERARGARGDD183 - 2561 - 74
14ASNASNARGARGBB185 - 2563 - 74
24ASNASNARGARGCC185 - 2563 - 74
15METMETARGARGBB184 - 2562 - 74
25METMETARGARGDD184 - 2562 - 74
16ASNASNARGARGCC185 - 2563 - 74
26ASNASNARGARGDD185 - 2563 - 74

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Far upstream element-binding protein 1 / FUSE-binding protein 1 / DNA helicase V / hDH V


Mass: 8330.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96AE4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2M ammonium sulfate, 5% 2-propanol, 2.5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.9→49.4 Å / Num. obs: 18030 / % possible obs: 99 % / Redundancy: 3.9 % / CC1/2: 0.99 / Net I/σ(I): 5.3
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1152 / CC1/2: 0.719

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LIJ

4lij


Resolution: 1.9→49.36 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.985 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.167
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 892 5 %RANDOM
Rwork0.1954 ---
obs0.1978 17114 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.66 Å2 / Biso mean: 26.096 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å20.13 Å2
2---0.38 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.9→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 26 100 2202
Biso mean--73.89 28.57 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132124
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172152
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6452851
X-RAY DIFFRACTIONr_angle_other_deg1.3871.5845016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6765276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93724.94387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45915431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.011510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022276
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02326
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A17680.17
12B17680.17
21A15540.15
22C15540.15
31A17660.16
32D17660.16
41B15360.18
42C15360.18
51B19030.14
52D19030.14
61C16070.19
62D16070.19
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 61 -
Rwork0.24 1269 -
all-1330 -
obs--99.03 %
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)
11.27450.23190.08832.5048-0.09382.8542-0.0532-0.04220.1696-0.13140.00050.1641-0.1803-0.03830.05270.09190.00710.02130.002-0.00390.05069.09821.018244.1049
22.2058-0.29940.41031.97970.92012.2489-0.0456-0.1646-0.06230.0068-0.01270.13230.0247-0.10060.05830.0839-0.00180.0530.0147-0.00040.0429.39370.63849.512
30.9467-0.91610.45221.9752-0.71011.90630.03430.07010.0007-0.0021-0.07330.10160.0904-0.04530.0390.0786-0.01550.03790.0118-0.00970.026110.9331-8.652531.2487
41.74960.2597-0.11771.3874-0.42550.9024-0.04450.0880.0177-0.06380.00450.05190.0393-0.06170.040.0652-0.00550.02980.02250.00280.0268.768312.438425.5505
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A183 - 256
2X-RAY DIFFRACTION2B183 - 256
3X-RAY DIFFRACTION3C184 - 258
4X-RAY DIFFRACTION4D183 - 256

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