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- PDB-2v7d: 14-3-3 protein zeta in complex with Thr758 phosphorylated integri... -

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Basic information

Entry
Database: PDB / ID: 2v7d
Title14-3-3 protein zeta in complex with Thr758 phosphorylated integrin beta2 peptide
Components
  • 14-3-3 PROTEIN ZETA/DELTA
  • INTEGRIN BETA CHAIN, BETA 2 VARIANT
KeywordsSIGNALING PROTEIN / MEMBRANE / INTEGRIN / RECEPTOR / CYTOPLASM / ACETYLATION / TRANSMEMBRANE / BETA2 INTEGRIN / PHOSPHORYLATION / DISEASE MUTATION / PYRROLIDONE CARBOXYLIC ACID / 14-3-3 ZETA / GLYCOPROTEIN / CELL ADHESION
Function / homology
Function and homology information


KSRP (KHSRP) binds and destabilizes mRNA / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / integrin alphaX-beta2 complex / GP1b-IX-V activation signalling / positive regulation of neutrophil degranulation / cellular extravasation ...KSRP (KHSRP) binds and destabilizes mRNA / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / integrin alphaX-beta2 complex / GP1b-IX-V activation signalling / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / Deactivation of the beta-catenin transactivating complex / ICAM-3 receptor activity / regulation of programmed cell death / synaptic target recognition / Rap1 signalling / TP53 Regulates Metabolic Genes / Golgi reassembly / : / complement component C3b binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response / neutrophil migration / establishment of Golgi localization / respiratory system process / tube formation / regulation of synapse maturation / negative regulation of protein localization to nucleus / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / negative regulation of dopamine metabolic process / receptor clustering / endodermal cell differentiation / amyloid-beta clearance / tertiary granule membrane / plasma membrane raft / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / positive regulation of protein targeting to membrane / phosphoserine residue binding / Integrin cell surface interactions / endothelial cell migration / regulation of ERK1 and ERK2 cascade / protein targeting / specific granule membrane / cellular response to glucose starvation / positive regulation of superoxide anion generation / cell adhesion molecule binding / heat shock protein binding / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / neutrophil chemotaxis / receptor-mediated endocytosis / lung development / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / receptor internalization / integrin binding / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / intracellular protein localization / melanosome / cell-cell signaling / extracellular vesicle / regulation of cell shape / amyloid-beta binding / angiogenesis / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / transmembrane transporter binding / protein phosphorylation / receptor complex / cell adhesion / inflammatory response / protein domain specific binding / external side of plasma membrane / focal adhesion / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / protein kinase binding / glutamatergic synapse / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction
Similarity search - Function
Integrin beta-2 subunit / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. ...Integrin beta-2 subunit / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / 14-3-3 domain / Integrin domain superfamily / Delta-Endotoxin; domain 1 / PSI domain / domain found in Plexins, Semaphorins and Integrins / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Integrin beta-2 / 14-3-3 protein zeta/delta / Integrin beta-2
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTakala, H. / Ylanne, J.
CitationJournal: Blood / Year: 2008
Title: Beta2 Integrin Phosphorylation on Thr758 Acts as a Molecular Switch to Regulate 14-3-3 and Filamin Binding.
Authors: Takala, H. / Nurminen, E. / Nurmi, S.M. / Aatonen, M. / Strandin, T. / Takatalo, M. / Kiema, T. / Gahmberg, C.G. / Ylanne, J. / Fagerholm, S.C.
History
DepositionJul 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 PROTEIN ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
C: 14-3-3 PROTEIN ZETA/DELTA
D: 14-3-3 PROTEIN ZETA/DELTA
P: INTEGRIN BETA CHAIN, BETA 2 VARIANT
Q: INTEGRIN BETA CHAIN, BETA 2 VARIANT
R: INTEGRIN BETA CHAIN, BETA 2 VARIANT
S: INTEGRIN BETA CHAIN, BETA 2 VARIANT


Theoretical massNumber of molelcules
Total (without water)116,2068
Polymers116,2068
Non-polymers00
Water2,792155
1
A: 14-3-3 PROTEIN ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
P: INTEGRIN BETA CHAIN, BETA 2 VARIANT
Q: INTEGRIN BETA CHAIN, BETA 2 VARIANT


Theoretical massNumber of molelcules
Total (without water)58,1034
Polymers58,1034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-15.2 kcal/mol
Surface area27450 Å2
MethodPQS
2
C: 14-3-3 PROTEIN ZETA/DELTA
D: 14-3-3 PROTEIN ZETA/DELTA
R: INTEGRIN BETA CHAIN, BETA 2 VARIANT
S: INTEGRIN BETA CHAIN, BETA 2 VARIANT


Theoretical massNumber of molelcules
Total (without water)58,1034
Polymers58,1034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-15.9 kcal/mol
Surface area27370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)94.920, 94.920, 233.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.50828, -0.86054, 0.03351), (-0.8607, -0.50892, -0.01416), (0.02924, -0.02164, -0.99934)15.60104, 28.84008, 37.94756
2given(-0.99912, -0.00193, -0.04191), (0.00357, -0.99923, -0.0391), (-0.0418, -0.03922, 0.99836)90.95183, -12.81278, 1.68186
3given(-0.51182, 0.859, 0.01229), (0.85838, 0.51077, 0.04797), (0.03493, 0.0351, -0.99877)73.8293, -42.9194, 37.86885
4given(0.49414, -0.86862, 0.03652), (-0.86893, -0.4948, -0.01143), (0.02799, -0.02608, -0.99927)16.06685, 29.00972, 38.02059
5given(-0.99855, -0.00868, -0.05314), (0.00975, -0.99975, -0.01988), (-0.05296, -0.02037, 0.99839)91.34393, -13.70368, 1.85822
6given(-0.51133, 0.85911, -0.02175), (0.8574, 0.5117, 0.05496), (0.05835, 0.00945, -0.99825)74.85167, -43.02853, 36.97404
7given(0.46424, -0.88534, 0.02568), (-0.88529, -0.46472, -0.01724), (0.0272, -0.01473, -0.99952)17.68635, 28.9548, 37.66203
8given(-0.99572, -0.01462, -0.09131), (0.01748, -0.99938, -0.03065), (-0.09081, -0.03211, 0.99535)92.4905, -13.55276, 3.3659
9given(-0.4603, 0.88575, -0.0597), (0.88598, 0.4626, 0.03241), (0.05633, -0.03798, -0.99769)73.95686, -42.11787, 38.08175
10given(0.48272, -0.87312, 0.06813), (-0.87411, -0.48514, -0.02392), (0.05393, -0.048, -0.99739)15.59743, 29.26708, 37.61781
11given(-0.99852, 0.02806, -0.04667), (-0.02673, -0.99923, -0.02882), (-0.04745, -0.02753, 0.99849)90.17595, -12.3777, 1.67921
12given(-0.51279, 0.85846, -0.00982), (0.85768, 0.51277, 0.03815), (0.03778, 0.01114, -0.99922)74.33581, -42.43333, 37.95855

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Components

#1: Protein
14-3-3 PROTEIN ZETA/DELTA / PROTEIN KINASE C INHIBITOR PROTEIN 1 / KCIP-1 / FACTOR ACTIVATING EXOENZYME S / FAS


Mass: 27921.221 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63103
#2: Protein/peptide
INTEGRIN BETA CHAIN, BETA 2 VARIANT / THR758 PHOPHORYLATED BETA2 INTEGRIN PEPTIDE


Mass: 1130.186 Da / Num. of mol.: 4 / Fragment: INTEGRIN CYTOPLASMIC TAIL, RESIDUES 755-764 / Source method: obtained synthetically / Details: THR758 SIDE CHAIN PHOSPHORYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q53HS5, UniProt: P05107*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Compound detailsADAPTER PROTEIN IMPLICATED IN THE REGULATION OF A LARGE SPECTRUM OF BOTH GENERAL AND SPECIALIZED ...ADAPTER PROTEIN IMPLICATED IN THE REGULATION OF A LARGE SPECTRUM OF BOTH GENERAL AND SPECIALIZED SIGNALING PATHWAY
Has protein modificationY
Sequence detailsRESIDUES (-1-0) ARE REMNANTS OF A FUSION PROTEIN AND A PART OF ONLY THIS STRUCTURE

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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: 2.84 Å3/Da / Density % sol: 56.32 % / Description: NONE
Crystal growpH: 8.5
Details: 18-19% PEG3350, 10MM CACL2, 1MM NICL2, 100MM TRIS PH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.5→500.1 Å / Num. obs: 40994 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.09 / Net I/σ(I): 16.86
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.94 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.91 / Rsym value: 0.534 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4O

1a4o


Resolution: 2.5→47.6 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINTS / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: LEAST SQUARES RESIDUAL FOR HEMIHEDRAL TWINNING
Details: USED TWINNING FRACTION 0.306. TWINNING OPERATOR H,-H-K,-L
RfactorNum. reflection% reflectionSelection details
Rfree0.2733 1967 4.8 %RANDOM
Rwork0.2277 ---
obs0.2277 39003 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.04 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 65.1 Å2
Baniso -1Baniso -2Baniso -3
1--17.12 Å20 Å20 Å2
2---17.12 Å20 Å2
3---34.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati sigma a0.85 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7490 0 0 155 7645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007856
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.16854
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.9308
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.70783
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4078 181 0.047 %
Rwork0.3983 3889 -
obs--0.9981 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP_TPO4.PARAM / Topol file: PROTEIN_TPO3.TOP

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