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- PDB-4h22: Crystal structure of the dimeric coiled-coil domain of the cytoso... -

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Basic information

Entry
Database: PDB / ID: 4h22
TitleCrystal structure of the dimeric coiled-coil domain of the cytosolic nucleic acid sensor LRRFIP1
ComponentsLeucine-rich repeat flightless-interacting protein 1
KeywordsTRANSCRIPTION / nucleic acid sensor / Flightless-1
Function / homology
Function and homology information


LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of type I interferon production / Signaling by FGFR1 in disease / DNA-binding transcription repressor activity, RNA polymerase II-specific / double-stranded RNA binding / positive regulation of NF-kappaB transcription factor activity / cytoskeleton / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of type I interferon production / Signaling by FGFR1 in disease / DNA-binding transcription repressor activity, RNA polymerase II-specific / double-stranded RNA binding / positive regulation of NF-kappaB transcription factor activity / cytoskeleton / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Leucine-rich repeat flightless-interacting protein 1/2 / LRRFIP family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4090 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Leucine-rich repeat flightless-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsNguyen, J.B. / Modis, Y.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structure of the dimeric coiled-coil domain of the cytosolic nucleic acid sensor LRRFIP1.
Authors: Nguyen, J.B. / Modis, Y.
History
DepositionSep 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat flightless-interacting protein 1
B: Leucine-rich repeat flightless-interacting protein 1
C: Leucine-rich repeat flightless-interacting protein 1
D: Leucine-rich repeat flightless-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)49,6004
Polymers49,6004
Non-polymers00
Water46826
1
A: Leucine-rich repeat flightless-interacting protein 1
B: Leucine-rich repeat flightless-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)24,8002
Polymers24,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-44 kcal/mol
Surface area12680 Å2
MethodPISA
2
C: Leucine-rich repeat flightless-interacting protein 1
D: Leucine-rich repeat flightless-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)24,8002
Polymers24,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-40 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.363, 71.447, 68.035
Angle α, β, γ (deg.)90.00, 110.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Leucine-rich repeat flightless-interacting protein 1 / LRR FLII-interacting protein 1 / GC-binding factor 2 / TAR RNA-interacting protein


Mass: 12399.946 Da / Num. of mol.: 4 / Fragment: UNP residues 162-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRFIP1, GCF2, TRIP / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q32MZ4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, MES pH 6.5, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. all: 15508 / Num. obs: 15465 / % possible obs: 99.7 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8
Reflection shellResolution: 2.89→2.94 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2q6q

2q6q


Resolution: 2.89→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.923 / SU B: 29.59 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 1.8 / ESU R: 0.434 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24757 775 5 %RANDOM
Rwork0.23461 ---
obs0.23529 14690 99.1 %-
all-15465 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.862 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å2-0 Å2-0.12 Å2
2---0.04 Å2-0 Å2
3---5.37 Å2
Refinement stepCycle: LAST / Resolution: 2.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 0 26 2656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022662
X-RAY DIFFRACTIONr_angle_refined_deg0.91.9613546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3155308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.44826.025161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.78315563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.811514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022002
LS refinement shellResolution: 2.89→2.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 56 -
Rwork0.357 980 -
obs--93.42 %
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)
13.985-2.0131.96621.0622-0.97611.16520.1845-0.20410.1015-0.1283-0.0268-0.06310.1968-0.1351-0.15770.07840.0461-0.08630.25860.01720.1764-0.28198.7795-20.8824
20.9733-0.86390.50521.2715-0.71411.13650.1311-0.0249-0.0202-0.0645-0.1203-0.09610.25970.0798-0.01080.11640.0190.01730.15340.05370.1376-1.0957.0633-21.7395
31.4908-2.2001-0.49883.55760.75940.1991-0.0536-0.1409-0.0274-0.12940.12360.07-0.00610.0241-0.070.12820.056-0.0070.1749-0.00520.171-25.58117.7081-23.4163
44.6931-5.1966-1.50366.26291.88090.66990.094-0.3437-0.1738-0.32380.08080.0811-0.12860.0249-0.17480.070.08310.05120.17240.02790.263-24.99516.7117-19.4822
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A168 - 248
2X-RAY DIFFRACTION2B167 - 249
3X-RAY DIFFRACTION3C170 - 243
4X-RAY DIFFRACTION4D170 - 243

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