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- PDB-4fxv: Crystal structure of an ELAV-like protein 1 (ELAVL1) from Homo sa... -

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Basic information

Entry
Database: PDB / ID: 4fxv
TitleCrystal structure of an ELAV-like protein 1 (ELAVL1) from Homo sapiens at 1.90 A resolution
ComponentsELAV-like protein 1
KeywordsRNA BINDING PROTEIN / TRANSCRIPTION / RNA recognition motif / putative RNA-binding domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


post-transcriptional gene silencing / negative regulation of miRNA-mediated gene silencing / HuR (ELAVL1) binds and stabilizes mRNA / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / miRNA binding / lncRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization ...post-transcriptional gene silencing / negative regulation of miRNA-mediated gene silencing / HuR (ELAVL1) binds and stabilizes mRNA / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / miRNA binding / lncRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization / sarcoplasm / positive regulation of superoxide anion generation / mRNA 3'-UTR binding / positive regulation of translation / P-body / protein homooligomerization / cytoplasmic stress granule / protein import into nucleus / double-stranded RNA binding / cytoplasmic vesicle / postsynapse / ribonucleoprotein complex / mRNA binding / glutamatergic synapse / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily ...HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of an ELAV-like protein 1 (ELAVL1) from Homo sapiens at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn / software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELAV-like protein 1
B: ELAV-like protein 1
C: ELAV-like protein 1
D: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)45,1664
Polymers45,1664
Non-polymers00
Water5,711317
1
A: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)11,2911
Polymers11,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)11,2911
Polymers11,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)11,2911
Polymers11,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ELAV-like protein 1


Theoretical massNumber of molelcules
Total (without water)11,2911
Polymers11,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.436, 73.436, 272.957
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-102-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
ELAV-like protein 1 / Hu-antigen R / HuR


Mass: 11291.405 Da / Num. of mol.: 4 / Fragment: RRM 1 domain residues 20-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC003376, ELAVL1, HUR / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q15717
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 20-99) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.35 Å3/Da / Density % sol: 47.71 %
Description: THE DATA COLLECTION STATISTICS IN REMARK 200 ABOVE ARE BEFORE THE REJECTION OF 309 UNUSUALLY STRONG REFLECTIONS WITH I/ > 15, MOSTLY NEAR ICE RINGS AT RESOLUTION 2.25A, 2.24A 3.46A AND 2. ...Description: THE DATA COLLECTION STATISTICS IN REMARK 200 ABOVE ARE BEFORE THE REJECTION OF 309 UNUSUALLY STRONG REFLECTIONS WITH I/ > 15, MOSTLY NEAR ICE RINGS AT RESOLUTION 2.25A, 2.24A 3.46A AND 2.64A, WHICH WERE EXCLUDED FROM THE FINAL REFINEMENT.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.200M NH4Cl, 20.00% PEG-3350, No Buffer pH 6.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97923
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 15, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.9→28.823 Å / Num. all: 34829 / Num. obs: 34829 / % possible obs: 97.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 17.877 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.14 / Rsym value: 0.132 / Net I/av σ(I): 3.328 / Net I/σ(I): 11.2 / Num. measured all: 352640
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-1.956.90.5250.4822.61525222190.1990.5250.4822.687.4
1.95-290.5230.4933.82218024700.170.5230.4933.899.3
2-2.0610.80.4320.4125.22625124290.130.4320.4125.2100
2.06-2.1210.80.3510.3346.32571123710.1050.3510.3346.3100
2.12-2.1910.80.3240.3096.82475522890.0970.3240.3096.8100
2.19-2.2790.3140.2925.91676118600.110.3140.2925.984.3
2.27-2.3610.80.250.2388.22353921880.0750.250.2388.2100
2.36-2.4510.80.1950.18610.12244820850.0590.1950.18610.1100
2.45-2.5610.80.1690.16111.22140219820.0510.1690.16111.2100
2.56-2.6910.80.1580.15122072719220.0480.1580.1512100
2.69-2.8310.70.1330.12713.81981218500.0410.1330.12713.8100
2.83-310.80.1150.1115.61859817300.0350.1150.1115.6100
3-3.2110.60.110.10416.81761616620.0330.110.10416.8100
3.21-3.4710.50.1060.118.81629315470.0320.1060.118.8100
3.47-3.89.80.1220.11619.11366313900.0390.1220.11619.197.7
3.8-4.2510.30.0850.0821.11357113240.0260.0850.0821.1100
4.25-4.9110.20.0760.07321.91208411820.0230.0760.07321.9100
4.91-6.01100.0820.07820.81012810160.0260.0820.07820.8100
6.01-8.59.60.0740.07120.578458210.0230.0740.07120.599.9
8.5-28.8238.10.0620.05820.440044920.020.0620.05820.495.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.823 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.094 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 309 UNUSUALLY STRONG REFLECTIONS WITH I/ > 15, MOSTLY NEAR ICE RINGS AT RESOLUTION 2.25A, 2.24A, 3.46A AND 2.64A, WERE EXCLUDED FROM THE FINAL REFINEMENT. 6. EXPERIMENTAL PHASES (SAD) WERE USED AS RESTRAINTS DURING STRUCTURE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1684 5.1 %RANDOM
Rwork0.2015 31587 --
obs0.2032 33271 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.5626 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.51 Å20 Å2
2--1.03 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 0 317 2809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192638
X-RAY DIFFRACTIONr_bond_other_d0.0010.021783
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9633588
X-RAY DIFFRACTIONr_angle_other_deg1.05134347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7945351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34723.81126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31215461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4591523
X-RAY DIFFRACTIONr_chiral_restr0.1030.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.663 89 -
Rwork0.664 1645 -
all-1734 -
obs--73.94 %
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)
13.54580.60170.82064.98351.05675.96050.0346-0.195-0.05130.2046-0.0325-0.01050.1094-0.0009-0.00210.1117-0.0027-0.03080.01130.00530.0335-9.840649.16246.5886
21.95620.37440.45324.97051.61445.5439-0.01480.0071-0.0206-0.00230.07330.19480.4383-0.0364-0.05840.19410.0182-0.04350.02820.00990.0969-9.332651.971231.9972
34.3953-1.2764-0.7854.40610.61144.43230.0598-0.0819-0.08580.01260.013-0.04940.228-0.0744-0.07280.0705-0.00990.00870.0082-0.00670.0268-11.133272.701513.6955
44.6452-0.1718-0.33155.06580.78554.01440.0692-0.1746-0.03060.24410.1332-0.5220.32910.5945-0.20230.14750.0622-0.05530.1578-0.06540.17477.022159.824440.6779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 99
2X-RAY DIFFRACTION2B-2 - 97
3X-RAY DIFFRACTION3C-3 - 99
4X-RAY DIFFRACTION4D0 - 96

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