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- PDB-3dvg: Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked... -

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Basic information

Entry
Database: PDB / ID: 3dvg
TitleCrystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin
Components
  • Human IgG1 fab fragment heavy chain
  • Human IgG1 fab fragment light chain
  • Ubiquitin
  • Ubiquitin D77
KeywordsIMMUNE SYSTEM / di-ubiquitin / fab fragment / antibody / Nucleus / Phosphoprotein / Ribosomal protein
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation ...: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / cytosolic ribosome / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Iron uptake and transport / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD
Similarity search - Function
: / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / : / Ubiquitin domain signature. ...: / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ubiquitin-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHymowitz, S.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.
Authors: Newton, K. / Matsumoto, M.L. / Wertz, I.E. / Kirkpatrick, D.S. / Lill, J.R. / Tan, J. / Dugger, D. / Gordon, N. / Sidhu, S.S. / Fellouse, F.A. / Komuves, L. / French, D.M. / Ferrando, R.E. / ...Authors: Newton, K. / Matsumoto, M.L. / Wertz, I.E. / Kirkpatrick, D.S. / Lill, J.R. / Tan, J. / Dugger, D. / Gordon, N. / Sidhu, S.S. / Fellouse, F.A. / Komuves, L. / French, D.M. / Ferrando, R.E. / Lam, C. / Compaan, D. / Yu, C. / Bosanac, I. / Hymowitz, S.G. / Kelley, R.F. / Dixit, V.M.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human IgG1 fab fragment light chain
B: Human IgG1 fab fragment heavy chain
X: Ubiquitin D77
Y: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)66,1834
Polymers66,1834
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.806, 88.117, 90.226
Angle α, β, γ (deg.)90.00, 108.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Human IgG1 fab fragment light chain


Mass: 23731.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Gene: fab fragment light chain / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PIL8*PLUS
#2: Antibody Human IgG1 fab fragment heavy chain


Mass: 24590.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Gene: fab fragment light chain / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
#3: Protein Ubiquitin D77


Mass: 8974.193 Da / Num. of mol.: 1 / Mutation: D77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS
#4: Protein Ubiquitin


Mass: 8887.120 Da / Num. of mol.: 1 / Mutation: K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: protein: 17.0 mg/mL in 20 mM Tris-HCl pH 7.3, 150 mM NaCl well solution: 0.1M Tris-HCl pH 8.0, 1.6M LiS04 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 24012 / Num. obs: 24012 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.051
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2380 / Rsym value: 0.58 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 29.626 / SU ML: 0.287 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.666 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26079 2441 10.2 %RANDOM
Rwork0.21917 ---
obs0.22355 21569 97.91 %-
all-21569 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.091 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 0 25 4491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224564
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9636196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82724.309181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51215772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4861522
X-RAY DIFFRACTIONr_chiral_restr0.0780.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023388
X-RAY DIFFRACTIONr_nbd_refined0.1930.21693
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2152
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.25
X-RAY DIFFRACTIONr_mcbond_it2.1412.52977
X-RAY DIFFRACTIONr_mcangle_it3.35754686
X-RAY DIFFRACTIONr_scbond_it2.1592.51821
X-RAY DIFFRACTIONr_scangle_it3.12451510
LS refinement shellResolution: 2.6→2.655 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.425 139 -
Rwork0.317 1231 -
obs--94.16 %
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)
12.763-0.02050.76315.094-0.17151.40260.0515-0.10770.19450.05620.04750.3214-0.08320.1254-0.099-0.4661-0.1367-0.14980.02360.0439-0.21597.117640.559119.188
22.83731.2816-0.16523.4934-0.17082.40870.12320.0070.03290.1583-0.30560.24860.1058-0.23290.1823-0.5061-0.1088-0.1956-0.0205-0.0137-0.0942-19.563121.86487.4817
35.795-1.3352-1.03247.93421.82725.45640.1045-0.80640.50030.89260.3367-0.7035-0.60180.5376-0.4412-0.1063-0.2677-0.33870.4029-0.0667-0.1229.609651.176135.3372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 109
2X-RAY DIFFRACTION1B1 - 112
3X-RAY DIFFRACTION2A110 - 214
4X-RAY DIFFRACTION2B113 - 221
5X-RAY DIFFRACTION3X1 - 73
6X-RAY DIFFRACTION3Y1 - 76

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