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- PDB-3vdz: Tailoring Encodable Lanthanide-Binding Tags as MRI Contrast Agent... -

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Entry
Database: PDB / ID: 3vdz
TitleTailoring Encodable Lanthanide-Binding Tags as MRI Contrast Agents: xq-dSE3-Ubiquitin at 2.4 Angstroms
ComponentsUbiquitin-40S ribosomal protein S27a
KeywordsMETAL BINDING PROTEIN / DE NOVO DESIGN / Gadolinium / MRI contrast agent / peptide-based contrast agent / lanthanide binding tag
Function / homology
Function and homology information


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 ...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 / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of BACH1 activity / Regulation of PTEN localization / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Gap-filling DNA repair synthesis and ligation in GG-NER / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / cytosolic ribosome / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Degradation of DVL / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Recognition of DNA damage by PCNA-containing replication complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Termination of translesion DNA synthesis / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Degradation of AXIN / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis
Similarity search - Function
Rhinovirus 14, subunit 4 - #180 / Rhinovirus 14, subunit 4 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. ...Rhinovirus 14, subunit 4 - #180 / Rhinovirus 14, subunit 4 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Few Secondary Structures / Irregular / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
GADOLINIUM ATOM / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciessynthetic construct (others)
homo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.4 Å
AuthorsDaughtry, K.D. / Martin, L.J. / Surraju, A. / Imperiali, B. / Allen, K.N.
CitationJournal: Chembiochem / Year: 2012
Title: Tailoring encodable lanthanide-binding tags as MRI contrast agents.
Authors: Daughtry, K.D. / Martin, L.J. / Sarraju, A. / Imperiali, B. / Allen, K.N.
History
DepositionJan 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Oct 21, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns_shell ...pdbx_struct_conn_angle / reflns_shell / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-40S ribosomal protein S27a
B: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,40010
Polymers24,3872
Non-polymers1,0138
Water73941
1
A: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7005
Polymers12,1931
Non-polymers5074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7005
Polymers12,1931
Non-polymers5074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.166, 46.166, 113.552
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 12193.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct, homo sapiens / Plasmid: pET11-a / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express cells / References: UniProt: P62987*PLUS
#2: Chemical
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Gd
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE C-TERMINAL PORTION OF CRYSTALLIZED SEQUENCE (SEE REMARK SEQRES) CORRESPONDS TO A SECTION OF THE ...THE C-TERMINAL PORTION OF CRYSTALLIZED SEQUENCE (SEE REMARK SEQRES) CORRESPONDS TO A SECTION OF THE UNP ENTRY P62979 (RESIDUES RANGE 101-175)

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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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M MES pH 5.0, 0.3 M ammonium sulfate, 19% poly(ethylene) glycol 8000 and 20 % glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 15, 2009 / Details: Helios optics
RadiationMonochromator: rotating-anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 5.17 % / Av σ(I) over netI: 45.85 / Number: 101984 / Rsym value: 0.209 / D res high: 1.7 Å / Num. obs: 19728 / % possible obs: 66.49
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRsym value
2.913.6610.211
2.542.9110.278
2.312.5410.384
2.142.3110.444
2.022.1410.498
1.912.0210.583
ReflectionResolution: 2.4→39.98 Å / Num. all: 20445 / Num. obs: 20445 / % possible obs: 96.55 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.0503 / Net I/σ(I): 11.25
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.2706 / Mean I/σ(I) obs: 3.14 / % possible all: 90.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
SAINTV7.60Adata reduction
SOLVEphasing
PHENIXdev_940refinement
PDB_EXTRACT3.1data extraction
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→37.851 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7773 / SU ML: 0.35 / σ(F): 2 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 1031 10.28 %Random
Rwork0.2233 ---
obs0.228 10447 96.48 %-
all-10447 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.014 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 47.73 Å2 / Biso mean: 28.5558 Å2 / Biso min: 20.54 Å2
Baniso -1Baniso -2Baniso -3
1-4.8664 Å2-0 Å2-0 Å2
2--4.8664 Å2-0 Å2
3----9.7327 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 24 41 1767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121734
X-RAY DIFFRACTIONf_angle_d1.372344
X-RAY DIFFRACTIONf_chiral_restr0.098270
X-RAY DIFFRACTIONf_plane_restr0.005310
X-RAY DIFFRACTIONf_dihedral_angle_d14.397656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.45590.34271270.29431167129491
2.4559-2.51730.41561300.30411124125489
2.5173-2.58530.32841390.28141182132193
2.5853-2.66140.26951390.27461176131594
2.6614-2.74730.35241350.26771185132095
2.7473-2.84540.29831440.25991251139596
2.8454-2.95930.32831530.26941239139298
2.9593-3.0940.35781220.27461287140999
3.094-3.2570.29741480.24571233138199
3.257-3.46090.27871320.24241238137099
3.4609-3.72790.25861500.22912611411100
3.7279-4.10270.21731250.17541273139899
4.1027-4.69540.24561600.159812791439100
4.6954-5.91210.23711480.2051221136998
5.9121-37.85540.16521480.16081213136197

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