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- PDB-4giw: Crystal structure of the RUN domain of human NESCA -

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Basic information

Entry
Database: PDB / ID: 4giw
TitleCrystal structure of the RUN domain of human NESCA
ComponentsRUN and SH3 domain-containing protein 1
KeywordsSIGNALING PROTEIN / NGF-TrkA signaling pathway / NF-kB pathway
Function / homology
Function and homology information


protein polyubiquitination / microtubule cytoskeleton / actin binding / cytoplasmic vesicle / microtubule / postsynaptic density / early endosome / Golgi apparatus / nucleus / cytosol
Similarity search - Function
RUN domain / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Variant SH3 domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Src homology 3 domains / SH3-like domain superfamily ...RUN domain / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Variant SH3 domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RUN and SH3 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBai, L. / Sun, Q. / Jiang, T.
CitationJournal: Protein Cell / Year: 2012
Title: Crystal structure and functional implication of the RUN domain of human NESCA
Authors: Sun, Q. / Han, C. / Liu, L. / Wang, Y. / Deng, H. / Bai, L. / Jiang, T.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUN and SH3 domain-containing protein 1
B: RUN and SH3 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)43,6602
Polymers43,6602
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-7 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.116, 94.201, 44.602
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUN and SH3 domain-containing protein 1 / Nesca / New molecule containing SH3 at the carboxy-terminus


Mass: 21829.924 Da / Num. of mol.: 2 / Fragment: RUN domain / Mutation: L150M, L152M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NESCA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BVN2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.86 Å3/Da / Density % sol: 33.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v) PEG3350, 0.2M K2HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→35.7 Å / Num. all: 20352 / Num. obs: 20352 / % possible obs: 99.63 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.247 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2144 / % possible all: 99.42

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→35.7 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.873 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE WAS REFINED ALSO WITH PHENIX.
RfactorNum. reflection% reflectionSelection details
Rfree0.21233 1059 4.9 %RANDOM
Rwork0.20449 ---
all0.20488 20352 --
obs0.20488 20352 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.251 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20.01 Å2
2--0.51 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 0 149 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222740
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.9933712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4295345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03422.596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86715481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4441518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211960
X-RAY DIFFRACTIONr_mcbond_it0.6461.51740
X-RAY DIFFRACTIONr_mcangle_it1.22422795
X-RAY DIFFRACTIONr_scbond_it1.78331000
X-RAY DIFFRACTIONr_scangle_it2.8944.5917
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 69 -
Rwork0.209 1487 -
obs-1380 99.11 %

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