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- PDB-4kmd: Crystal structure of Sufud60-Gli1p -

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Basic information

Entry
Database: PDB / ID: 4kmd
TitleCrystal structure of Sufud60-Gli1p
Components
  • Sufu
  • Zinc finger protein GLI1
KeywordsPROTEIN BINDING/TRANSCRIPTION / protein peptide complex / PROTEIN BINDING-TRANSCRIPTION complex
Function / homology
Function and homology information


notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / smoothened signaling pathway involved in ventral spinal cord interneuron specification / smoothened signaling pathway involved in spinal cord motor neuron cell fate specification / positive regulation of cellular response to drug / maintenance of protein localization in organelle / regulation of hepatocyte proliferation / GLI-SUFU complex / regulation of cerebellar granule cell precursor proliferation / ventral midline development ...notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / smoothened signaling pathway involved in ventral spinal cord interneuron specification / smoothened signaling pathway involved in spinal cord motor neuron cell fate specification / positive regulation of cellular response to drug / maintenance of protein localization in organelle / regulation of hepatocyte proliferation / GLI-SUFU complex / regulation of cerebellar granule cell precursor proliferation / ventral midline development / epidermal cell differentiation / pituitary gland development / prostate gland development / proximal/distal pattern formation / positive regulation of cell cycle G1/S phase transition / cerebellar cortex morphogenesis / regulation of smoothened signaling pathway / dorsal/ventral pattern formation / positive regulation of smoothened signaling pathway / coronary vasculature development / ventricular septum development / aorta development / negative regulation of protein import into nucleus / dorsal/ventral neural tube patterning / smoothened signaling pathway / skin development / digestive tract morphogenesis / regulation of osteoblast differentiation / heart looping / ciliary base / spermatid development / axoneme / negative regulation of osteoblast differentiation / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of cardiac muscle cell proliferation / Hedgehog 'off' state / lung development / liver regeneration / ciliary tip / positive regulation of DNA replication / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of smoothened signaling pathway / neural tube closure / protein sequestering activity / negative regulation of canonical Wnt signaling pathway / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / response to wounding / beta-catenin binding / osteoblast differentiation / transcription corepressor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / microtubule binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / cilium / positive regulation of cell migration / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
C2H2-type zinc-finger protein GLI-like / Sufu, C-terminal domain / Suppressor of fused / Suppressor of fused, eukaryotic / Suppressor of fused C-terminal / Suppressor of fused, N-terminal / Suppressor of fused, C-terminal domain superfamily / Suppressor of Fused Gli/Ci N terminal binding domain / Suppressor of fused-like domain / Suppressor of fused protein (SUFU) ...C2H2-type zinc-finger protein GLI-like / Sufu, C-terminal domain / Suppressor of fused / Suppressor of fused, eukaryotic / Suppressor of fused C-terminal / Suppressor of fused, N-terminal / Suppressor of fused, C-terminal domain superfamily / Suppressor of Fused Gli/Ci N terminal binding domain / Suppressor of fused-like domain / Suppressor of fused protein (SUFU) / : / C2H2 zinc finger / Gyrase A; domain 2 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Zinc finger protein GLI1 / Suppressor of fused homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsZhang, Y. / Qi, X. / Zhang, Z. / Wu, G.
CitationJournal: Nat Commun / Year: 2013
Title: Structural insight into the mutual recognition and regulation between Suppressor of Fused and Gli/Ci.
Authors: Zhang, Y. / Fu, L. / Qi, X. / Zhang, Z. / Xia, Y. / Jia, J. / Jiang, J. / Zhao, Y. / Wu, G.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Experimental preparation
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sufu
B: Zinc finger protein GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7699
Polymers51,0622
Non-polymers7077
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sufu
B: Zinc finger protein GLI1
hetero molecules

A: Sufu
B: Zinc finger protein GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,53818
Polymers102,1244
Non-polymers1,41414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9340 Å2
ΔGint-41 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.830, 82.118, 149.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sufu / SUFUH


Mass: 49380.262 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-285, 346-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUFU, UNQ650/PRO1280 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UMX1
#2: Protein/peptide Zinc finger protein GLI1 / Glioma-associated oncogene / Oncogene GLI


Mass: 1681.829 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 112-128 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P08151
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNP RESIDUES 286-345 ARE DELETION.

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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: 2.13 Å3/Da / Density % sol: 42.32 % / Mosaicity: 0.571 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M Magnesium Chloride, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jan 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 47766 / % possible obs: 98.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.079 / Χ2: 1.008 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.767.30.48947691.0041100
1.76-1.837.30.34947621.0161100
1.83-1.917.30.243480811100
1.91-2.027.30.16947930.9971100
2.02-2.147.40.12447890.991100
2.14-2.317.40.09648111.0091100
2.31-2.547.30.08548341.0281100
2.54-2.917.30.09248431.016199.9
2.91-3.666.90.07547681.021197.3
3.66-506.40.05245891.001190.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0110refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KM8

4km8


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.13 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 2416 5.1 %RANDOM
Rwork0.1946 ---
obs0.196 47718 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.48 Å2 / Biso mean: 29.618 Å2 / Biso min: 4.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 44 223 3254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223114
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9634227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4965377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07624145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54915495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6551517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212384
X-RAY DIFFRACTIONr_mcbond_it0.511.51879
X-RAY DIFFRACTIONr_mcangle_it0.97823039
X-RAY DIFFRACTIONr_scbond_it1.34331235
X-RAY DIFFRACTIONr_scangle_it2.1994.51186
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 182 -
Rwork0.215 3351 -
all-3533 -
obs--100 %
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)
10.42230.1738-0.15210.5231-0.02561.4790.03760.04240.0180.00940.02450.006-0.07130.0936-0.06210.01240.00370.00630.04580.0040.0542-20.354815.338415.9858
215.2211-1.8123-0.92725.5891-1.76316.1879-0.0443-0.0643-0.4471-0.09540.12390.25510.2092-0.0866-0.07970.0501-0.02340.01730.05170.00410.0422-23.234914.950512.4725
30.51960.3315-0.39440.5268-0.14271.64760.01050.0486-0.00010.03210.01480.0018-0.07280.0689-0.02530.009700.00240.0273-0.00190.0174-21.690314.614318.0328
42.8401-0.26932.28217.3843-4.45974.3024-0.1260.1663-0.057-1.1039-0.3236-0.65010.57350.36150.44960.47250.08220.2770.1904-0.04690.4338-24.43162.971124.5234
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 480
2X-RAY DIFFRACTION2B119 - 128
3X-RAY DIFFRACTION3A602 - 817
4X-RAY DIFFRACTION3B201 - 206
5X-RAY DIFFRACTION4A501 - 506

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