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- PDB-8zxw: Crystal structure of the anti-phosphorylated peptide C7 Fab antib... -

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Basic information

Entry
Database: PDB / ID: 8zxw
TitleCrystal structure of the anti-phosphorylated peptide C7 Fab antibody with peptide bound
Components
  • Fab, heavy chain
  • Fab, light chain
  • RAC-gamma serine/threonine-protein kinase
KeywordsIMMUNE SYSTEM / phosphorylated peptide / antibody
Function / homology
Function and homology information


positive regulation of artery morphogenesis / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / AKT phosphorylates targets in the nucleus / RUNX2 regulates genes involved in cell migration / : / RAB GEFs exchange GTP for GDP on RABs / brain morphogenesis / AKT phosphorylates targets in the cytosol / positive regulation of vascular endothelial cell proliferation ...positive regulation of artery morphogenesis / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / AKT phosphorylates targets in the nucleus / RUNX2 regulates genes involved in cell migration / : / RAB GEFs exchange GTP for GDP on RABs / brain morphogenesis / AKT phosphorylates targets in the cytosol / positive regulation of vascular endothelial cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / Regulation of TP53 Activity through Association with Co-factors / Co-inhibition by CTLA4 / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of PERK-mediated unfolded protein response / negative regulation of cellular senescence / Regulation of localization of FOXO transcription factors / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of cell size / positive regulation of TOR signaling / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Cyclin E associated events during G1/S transition / Downregulation of ERBB2:ERBB3 signaling / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / positive regulation of endothelial cell proliferation / FLT3 Signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / homeostasis of number of cells within a tissue / VEGFR2 mediated vascular permeability / TP53 Regulates Metabolic Genes / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / positive regulation of angiogenesis / Regulation of TP53 Degradation / G beta:gamma signalling through PI3Kgamma / PIP3 activates AKT signaling / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cilium / ciliary basal body / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Protein kinase B gamma, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. ...Protein kinase B gamma, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
RAC-gamma serine/threonine-protein kinase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsCaaveiro, J.M.M. / Kasahara, K. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K06962 Japan
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies.
Authors: Kasahara, K. / Kawade, R. / Nakakido, M. / Matsunaga, R. / Akiba, H. / Entzminger, K.C. / Maruyama, T. / Okumura, S.C.J. / Caaveiro, J.M.M. / Kuroda, D. / Tsumoto, K.
History
DepositionJun 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab, heavy chain
L: Fab, light chain
C: RAC-gamma serine/threonine-protein kinase
A: Fab, heavy chain
B: Fab, light chain
D: RAC-gamma serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4498
Polymers97,3226
Non-polymers1282
Water15,277848
1
H: Fab, heavy chain
L: Fab, light chain
C: RAC-gamma serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7534
Polymers48,6613
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-36 kcal/mol
Surface area19040 Å2
MethodPISA
2
A: Fab, heavy chain
B: Fab, light chain
D: RAC-gamma serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6964
Polymers48,6613
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-34 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.351, 67.841, 71.341
Angle α, β, γ (deg.)112.536, 104.989, 98.313
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide RAC-gamma serine/threonine-protein kinase / Protein kinase Akt-3 / Protein kinase B gamma / PKB gamma / RAC-PK-gamma / STK-2


Mass: 1505.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9Y243, non-specific serine/threonine protein kinase

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Antibody , 2 types, 4 molecules HALB

#1: Antibody Fab, heavy chain


Mass: 24387.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) / Strain (production host): EXPI293
#2: Antibody Fab, light chain


Mass: 22768.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) / Strain (production host): EXPI293

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Non-polymers , 3 types, 850 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium chloride 19% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→48.04 Å / Num. obs: 188006 / % possible obs: 93.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.027 / Net I/σ(I): 15.4
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6654 / CC1/2: 0.781 / Rpim(I) all: 0.296 / % possible all: 66.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDS20230630data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→48.04 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.537 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1653 9562 5.086 %
Rwork0.1369 178444 -
all0.138 --
obs-188006 93.531 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.556 Å2
Baniso -1Baniso -2Baniso -3
1-0.023 Å2-0.166 Å20.022 Å2
2---0.074 Å20.125 Å2
3----0.031 Å2
Refinement stepCycle: LAST / Resolution: 1.33→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6513 0 25 848 7386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166248
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.7889474
X-RAY DIFFRACTIONr_angle_other_deg0.5671.71814501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1465938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.496522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.046101031
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.52510251
X-RAY DIFFRACTIONr_chiral_restr0.0840.21142
X-RAY DIFFRACTIONr_chiral_restr_other0.0010.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021523
X-RAY DIFFRACTIONr_nbd_refined0.2280.21024
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.25563
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23379
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.23566
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2578
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.090.215
X-RAY DIFFRACTIONr_nbd_other0.2010.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.233
X-RAY DIFFRACTIONr_mcbond_it5.1381.953578
X-RAY DIFFRACTIONr_mcbond_other5.1361.953578
X-RAY DIFFRACTIONr_mcangle_it7.4953.4954477
X-RAY DIFFRACTIONr_mcangle_other7.4953.4954478
X-RAY DIFFRACTIONr_scbond_it5.4822.0923296
X-RAY DIFFRACTIONr_scbond_other5.4812.0923297
X-RAY DIFFRACTIONr_scangle_it8.0053.7664961
X-RAY DIFFRACTIONr_scangle_other8.0043.7674962
X-RAY DIFFRACTIONr_lrange_it12.1321.5817486
X-RAY DIFFRACTIONr_lrange_other11.92921.397400
X-RAY DIFFRACTIONr_rigid_bond_restr3.054313122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.3650.2255640.21210028X-RAY DIFFRACTION70.9017
1.365-1.4020.2177000.18612462X-RAY DIFFRACTION91.3457
1.402-1.4420.1897920.16612448X-RAY DIFFRACTION93.6152
1.442-1.4870.1836520.13912151X-RAY DIFFRACTION93.9601
1.487-1.5360.1586780.12611814X-RAY DIFFRACTION94.265
1.536-1.5890.1546310.11111554X-RAY DIFFRACTION94.6996
1.589-1.6490.1525890.10511212X-RAY DIFFRACTION95.0544
1.649-1.7170.1455820.10410739X-RAY DIFFRACTION95.3107
1.717-1.7930.155450.10410395X-RAY DIFFRACTION95.8136
1.793-1.880.1435710.1079947X-RAY DIFFRACTION95.9847
1.88-1.9820.1494980.1179480X-RAY DIFFRACTION96.3965
1.982-2.1020.1544440.1249035X-RAY DIFFRACTION96.4391
2.102-2.2470.1574070.1248524X-RAY DIFFRACTION96.9496
2.247-2.4260.1633680.1327982X-RAY DIFFRACTION97.0704
2.426-2.6570.1633290.1357327X-RAY DIFFRACTION97.1574
2.657-2.9690.1683550.1446628X-RAY DIFFRACTION97.1615
2.969-3.4270.1792920.1485826X-RAY DIFFRACTION97.2964
3.427-4.1910.182240.1524977X-RAY DIFFRACTION97.3423
4.191-5.9050.1562210.1473795X-RAY DIFFRACTION97.5468
5.905-48.040.1871200.1932121X-RAY DIFFRACTION97.7749

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