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- PDB-4nik: Structure of human Gankyrin in complex to the single chain antibody F5 -

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Basic information

Entry
Database: PDB / ID: 4nik
TitleStructure of human Gankyrin in complex to the single chain antibody F5
Components
  • 26S proteasome non-ATPase regulatory subunit 10
  • Single-chain Fv fragment antibody
KeywordsOncoprotein/Immune System / beta-hairpin-alpha-hairpin repeat / Oncoprotein / 26S proteasome / Oncoprotein-Immune System complex
Function / homology
Function and homology information


cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / protein localization to chromosome, telomeric region / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria ...cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / protein localization to chromosome, telomeric region / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of telomere capping / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / NAD+-protein poly-ADP-ribosyltransferase activity / cytoskeletal protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / protein localization to plasma membrane / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / positive regulation of cell growth / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / cytoskeleton / Ub-specific processing proteases / neuron projection / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSato, Y. / Weiss, E. / Rochel, N.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Restricted diversity of antigen binding residues of antibodies revealed by computational alanine scanning of 227 antibody-antigen complexes
Authors: Robin, G. / Sato, Y. / Desplancq, D. / Rochel, N. / Weiss, E. / Martineau, P.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references / Source and taxonomy
Revision 1.2Sep 23, 2015Group: Database references
Revision 1.3Nov 8, 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

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Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 10
B: Single-chain Fv fragment antibody


Theoretical massNumber of molelcules
Total (without water)51,7382
Polymers51,7382
Non-polymers00
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-7 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.578, 135.578, 68.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

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Components

#1: Protein 26S proteasome non-ATPase regulatory subunit 10 / 26S proteasome regulatory subunit p28 / Gankyrin / p28(GANK)


Mass: 24873.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD10 / Production host: Escherichia coli (E. coli) / References: UniProt: O75832
#2: Antibody Single-chain Fv fragment antibody


Mass: 26864.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: semi synthetic scFv / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 3.52 Å3/Da / Density % sol: 65.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 8% PEG8000, 0.1M Hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 1, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 25163 / Num. obs: 25163 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29.98 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOH, 3KFU

1uoh

3kfu


Resolution: 2.5→29.633 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8739 / SU ML: 0.61 / σ(F): 1.34 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1284 5.11 %random
Rwork0.1636 ---
all0.1658 25162 --
obs0.1658 25115 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.531 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 125.78 Å2 / Biso mean: 41.7502 Å2 / Biso min: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.9597 Å2-0 Å2-0 Å2
2--2.9597 Å2-0 Å2
3----5.9193 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 0 428 3847
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5003-2.60030.26631440.20982599274398
2.6003-2.71860.25171510.20022607275899
2.7186-2.86180.25011370.18492642277999
2.8618-3.04090.23481340.18942623275799
3.0409-3.27540.20591500.166526432793100
3.2754-3.60450.21541520.148226592811100
3.6045-4.12490.18571450.14382656280199
4.1249-5.19240.18521310.14132649278098
5.1924-29.63550.17191400.15362753289398
Refinement TLS params.Method: refined / Origin x: 4.0257 Å / Origin y: 55.9162 Å / Origin z: 29.7362 Å
111213212223313233
T0.084 Å20.0323 Å2-0.0138 Å2-0.061 Å20.0447 Å2--0.0728 Å2
L0.8452 °2-0.2557 °2-0.3265 °2-0.4999 °20.1369 °2--0.9138 °2
S-0.0107 Å °-0.1847 Å °-0.1543 Å °0.0184 Å °0.0045 Å °0.0588 Å °0.203 Å °0.1357 Å °0.034 Å °
Refinement TLS groupSelection details: ALL

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