[English] 日本語
Yorodumi
- PDB-4bla: Crystal structure of full-length human Suppressor of fused (SUFU)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bla
TitleCrystal structure of full-length human Suppressor of fused (SUFU) mutant lacking a regulatory subdomain (crystal form II)
ComponentsMALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
KeywordsSIGNALING PROTEIN / SUGAR BINDING PROTEIN-SIGNALING PROTEIN COMPLEX / HEDGEHOG GENE REGULATION / SIGNAL TRANSDUCTION / GLI / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


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 / GLI-SUFU complex / ciliary tip / coronary vasculature development / aorta development / ventricular septum development / negative regulation of protein import into nucleus / skin development ...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 / GLI-SUFU complex / ciliary tip / coronary vasculature development / aorta development / ventricular septum development / negative regulation of protein import into nucleus / skin development / ciliary base / detection of maltose stimulus / spermatid development / maltose transport complex / heart looping / carbohydrate transport / negative regulation of ubiquitin-dependent protein catabolic process / carbohydrate transmembrane transporter activity / maltose binding / negative regulation of osteoblast differentiation / maltose transport / maltodextrin transmembrane transport / Hedgehog 'off' state / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / negative regulation of smoothened signaling pathway / cell chemotaxis / negative regulation of DNA-binding transcription factor activity / neural tube closure / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / beta-catenin binding / transcription corepressor activity / outer membrane-bounded periplasmic space / periplasmic space / cilium / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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) / Gyrase A; domain 2 ...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) / Gyrase A; domain 2 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Suppressor of fused homolog
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCherry, A.L. / Finta, C. / Karlstrom, M. / Toftgard, R. / Jovine, L.
Citation
#1: Journal: Nat.Cell Biol. / Year: 1999
Title: Mammalian Suppressor-of-Fused Modulates Nuclear-Cytoplasmic Shuttling of GLI-1.
Authors: Kogerman, P. / Grimm, T. / Kogerman, L. / Krause, D. / Unden, A.B. / Sandstedt, B. / Toftgard, R. / Zaphiropoulos, P.G.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Characterization of the Physical Interaction of GLI Proteins with Sufu Proteins.
Authors: Dunaeva, M. / Michelson, P. / Kogerman, P. / Toftgard, R.
#3: Journal: Mol.Cell.Biol. / Year: 2004
Title: Suppressor of Fused Regulates GLI Activity Through a Dual Binding Mechanism.
Authors: Merchant, M. / Vajdos, F.F. / Ultsch, M. / Maun, H.R. / Wendt, U. / Cannon, J. / Desmarais, W. / Lazarus, R.A. / De Vos, A.M. / De Sauvage, F.J.
#4: Journal: Dev.Cell / Year: 2006
Title: Genetic Elimination of Suppressor of Fused Reveals an Essential Repressor Function in the Mammalian Hedgehog Signaling Pathway.
Authors: Svard, J. / Heby-Henricson, K. / Persson-Lek, M. / Rozell, B. / Lauth, M. / Bergstrom, A. / Ericson, J. / Toftgard, R. / Teglund, S.
History
DepositionMay 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
B: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
C: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
D: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG


Theoretical massNumber of molelcules
Total (without water)336,2194
Polymers336,2194
Non-polymers00
Water00
1
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG


Theoretical massNumber of molelcules
Total (without water)84,0551
Polymers84,0551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG


Theoretical massNumber of molelcules
Total (without water)84,0551
Polymers84,0551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG


Theoretical massNumber of molelcules
Total (without water)84,0551
Polymers84,0551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG


Theoretical massNumber of molelcules
Total (without water)84,0551
Polymers84,0551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.920, 372.570, 86.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG


Mass: 84054.734 Da / Num. of mol.: 4
Fragment: MBPP RESIDUES 29-387,SUFUH RESIDUES 32-278,361-483
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DELETION OF RESIDUES 279-360 AND REPLACEMENT WITH PSRGEDP LINKER
Source: (gene. exp.) ESCHERICHIA COLI (E. coli), (gene. exp.) HOMO SAPIENS (human)
Plasmid: PLJMBP4C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): JM109(DE3) / References: UniProt: P0AEX9, UniProt: Q9UMX1
Sequence detailsRESIDUES 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-278. RESIDUES 619- ...RESIDUES 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-278. RESIDUES 619-625 REPRESENT AN ARTIFICIAL LINKER. RESIDUES 626-748 REPRESENT UNIPROT Q9UMX1 RESIDUES 361-483.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.49 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN (11.6 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT) WAS CRYSTALLISED BY HANGING DROP VAPOUR DIFFUSION AT 4C WITH 0.1 M NA-HEPES PH 7.5, 17% (V/V) PEG 3350, 0.2 M NACL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.5→39.58 Å / Num. obs: 49033 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 110.826 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 28.1
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4BL8, 1OMP

4bl8

1omp


Resolution: 3.5→39.577 Å / SU ML: 0.61 / σ(F): 1.33 / Phase error: 32.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2932 2462 5.1 %
Rwork0.2591 --
obs0.2608 48733 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 177.658 Å2
Refinement stepCycle: LAST / Resolution: 3.5→39.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22889 0 0 0 22889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123501
X-RAY DIFFRACTIONf_angle_d1.24931968
X-RAY DIFFRACTIONf_dihedral_angle_d11.9038550
X-RAY DIFFRACTIONf_chiral_restr0.0583444
X-RAY DIFFRACTIONf_plane_restr0.0114171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.68450.42653620.39346432X-RAY DIFFRACTION98
3.6845-3.91510.37353580.35126473X-RAY DIFFRACTION99
3.9151-4.21710.32623410.29856514X-RAY DIFFRACTION100
4.2171-4.64090.26973330.24156587X-RAY DIFFRACTION100
4.6409-5.31110.25613400.22286626X-RAY DIFFRACTION100
5.3111-6.68610.30883460.25366715X-RAY DIFFRACTION100
6.6861-39.57940.2593820.22756924X-RAY DIFFRACTION100
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)
14.8187-1.1829-1.29545.62810.75973.629-0.55080.08670.2636-0.40940.8547-0.67130.0897-0.13540.00141.0003-0.28810.14251.19320.04641.101942.127677.3441-16.7246
23.8089-0.18562.66462.9543-1.06799.14550.064-0.7045-0.7481-0.22410.0711-0.71140.72960.48510.00030.5373-0.1095-0.04711.03150.1471.14332.083944.154211.6511
34.3198-1.3812-0.14115.7246-0.27636.2041-0.259-0.03720.05141.2606-0.0387-0.369-0.81460.6444-0.00021.1179-0.2686-0.15521.10520.12710.777717.986656.043945.0275
43.54890.0564-1.59876.7328-0.14076.22660.2602-0.0040.74322.609-0.8538-2.941-1.71390.6268-0.16162.1692-0.6489-0.96431.7360.53662.479942.43497.439735.815
55.01241.92761.78083.4118-0.01627.27340.22910.02230.319-0.2187-0.1470.2794-0.32670.2587-0.00040.85880.0094-0.04060.61150.07310.82168.50976.861713.5401
67.2872-0.1568-0.35233.22181.00915.9628-0.66960.4907-0.72-1.04630.38650.2064-0.3288-0.3941-00.9096-0.1971-0.11760.7925-0.07940.75942.520649.051-12.8553
75.09453.05241.44422.53121.7562.8632-0.2004-0.5865-0.55430.6277-0.24041.40711.3658-1.3486-0.0042.7163-0.68030.94881.98590.06272.7609-31.15944.552729.7252
82.0437-0.3454-0.19697.29822.81086.5643-0.088-0.0454-0.045-1.0896-0.11310.3951-0.60340.1406-0.00080.9025-0.2154-0.00810.56310.02810.761-2.531416.1177-4.2304
95.4107-1.17770.07653.73320.07386.1968-0.3205-0.06250.3235-0.55310.02660.00140.0402-0.47900.9769-0.1341-0.15970.94380.02320.6598-11.928632.7459-37.2202
101.5354-0.7488-0.62751.24310.29093.3189-0.15730.1272-1.5669-0.3299-0.54281.12291.4866-2.7672-0.23711.7285-0.2059-0.86744.1955-0.93652.8005-58.353627.9797-34.9012
112.8663-0.2046-0.06721.67560.60699.1734-0.3195-0.0839-0.1741-0.3947-0.33640.68-0.4811-1.7955-0.03840.68110.1383-0.13181.3912-0.25511.3299-29.803445.7984-5.8625
125.04041.24941.33936.4169-0.35177.0677-0.0775-0.3521-0.00260.7524-0.2790.065-0.1542-0.1158-0.00070.9013-0.0905-0.04970.67280.00070.6539-1.455246.443620.7237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID :371
2X-RAY DIFFRACTION2CHAIN A AND RESID 372:606
3X-RAY DIFFRACTION3CHAIN A AND RESID 607:
4X-RAY DIFFRACTION4CHAIN B AND RESID :371
5X-RAY DIFFRACTION5CHAIN B AND RESID 372:606
6X-RAY DIFFRACTION6CHAIN B AND RESID 607:
7X-RAY DIFFRACTION7CHAIN C AND RESID :371
8X-RAY DIFFRACTION8CHAIN C AND RESID 372:606
9X-RAY DIFFRACTION9CHAIN C AND RESID 607:
10X-RAY DIFFRACTION10CHAIN D AND RESID :371
11X-RAY DIFFRACTION11CHAIN D AND RESID 372:606
12X-RAY DIFFRACTION12CHAIN D AND RESID 607:

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more