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- PDB-1bt6: P11 (S100A10), LIGAND OF ANNEXIN II IN COMPLEX WITH ANNEXIN II N-... -

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Basic information

Entry
Database: PDB / ID: 1bt6
TitleP11 (S100A10), LIGAND OF ANNEXIN II IN COMPLEX WITH ANNEXIN II N-TERMINUS
Components
  • ANNEXIN II
  • S100A10
KeywordsCOMPLEX (LIGAND/ANNEXIN) / S100 FAMILY / EF-HAND PROTEIN / COMPLEX (LIGAND-ANNEXIN) / LIGAND OF ANNEXIN II / CALCIUM/PHOSPHOLIPID BINDING PROTEIN / COMPLEX (LIGAND-ANNEXIN) complex
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of cytosolic calcium levels / Dissolution of Fibrin Clot / phospholipase inhibitor activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / endocardial cell differentiation / growth plate cartilage development / positive regulation of plasma membrane repair ...voltage-gated calcium channel activity involved in regulation of cytosolic calcium levels / Dissolution of Fibrin Clot / phospholipase inhibitor activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / endocardial cell differentiation / growth plate cartilage development / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / positive regulation of chondrocyte differentiation / vesicle budding from membrane / plasma membrane protein complex / calcium-dependent phospholipid binding / positive regulation of calcium ion transport / Dissolution of Fibrin Clot / virion binding / vesicle membrane / phosphatidylserine binding / positive regulation of transforming growth factor beta receptor signaling pathway / bone mineralization / basement membrane / positive regulation of GTPase activity / positive regulation of exocytosis / positive regulation of focal adhesion assembly / regulation of neurogenesis / calcium ion homeostasis / cytoskeletal protein binding / positive regulation of stress fiber assembly / calcium channel complex / positive regulation of substrate adhesion-dependent cell spreading / Neutrophil degranulation / protein localization to plasma membrane / mRNA transcription by RNA polymerase II / calcium channel activity / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / : / vesicle / transmembrane transporter binding / calcium ion binding / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein S100-A10 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Protein S100-A10 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Protein S100-A10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRety, S. / Sopkova, J. / Renouard, M. / Osterloh, D. / Gerke, V. / Russo-Marie, F. / Lewit-Bentley, A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: The crystal structure of a complex of p11 with the annexin II N-terminal peptide.
Authors: Rety, S. / Sopkova, J. / Renouard, M. / Osterloh, D. / Gerke, V. / Tabaries, S. / Russo-Marie, F. / Lewit-Bentley, A.
History
DepositionSep 2, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 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: S100A10
B: S100A10
C: ANNEXIN II
D: ANNEXIN II


Theoretical massNumber of molelcules
Total (without water)25,1454
Polymers25,1454
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-65 kcal/mol
Surface area10320 Å2
MethodPISA
2
A: S100A10
B: S100A10
C: ANNEXIN II
D: ANNEXIN II

A: S100A10
B: S100A10
C: ANNEXIN II
D: ANNEXIN II


Theoretical massNumber of molelcules
Total (without water)50,2918
Polymers50,2918
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area13470 Å2
ΔGint-136 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.600, 56.400, 64.300
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.457998, -0.053155, -0.887363), (-0.024374, -0.997085, 0.072307), (-0.888619, 0.054745, 0.455367)133.80363, 54.89459, 78.87959
2given(-0.506522, 0.042448, -0.861181), (-0.119007, -0.99267, 0.021068), (-0.853975, 0.113158, 0.507861)133.22804, 64.91576, 72.08719

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Components

#1: Protein S100A10 / P11 / CALPACTIN LIGHT CHAIN


Mass: 11088.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET23A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60903
#2: Protein/peptide ANNEXIN II


Mass: 1483.706 Da / Num. of mol.: 2 / Fragment: N-TERMINAL
Source method: isolated from a genetically manipulated source
References: UniProt: P17785
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
250 mMTris-HCl11
31 mMdithiothreitol11
410 %PEG400012
510 %2-propanol12
6100 mMTris-HCl12

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 1998 / Details: FOCUSSING MONOCHROMATOR AND MONOLAYER
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→62 Å / Num. obs: 9774 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 6.25 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 20.6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.96 / Rsym value: 0.61
Reflection
*PLUS
Num. measured all: 29481
Reflection shell
*PLUS
Rmerge(I) obs: 0.61

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4P

1a4p


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.307 942 10 %RANDOM
Rwork0.228 ---
obs0.233 8511 96.8 %-
Displacement parametersBiso mean: 200.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 0 22 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0790.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it1.9762
X-RAY DIFFRACTIONp_mcangle_it3.1763
X-RAY DIFFRACTIONp_scbond_it3.263
X-RAY DIFFRACTIONp_scangle_it4.6354
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.2260.15
X-RAY DIFFRACTIONp_singtor_nbd0.3
X-RAY DIFFRACTIONp_multtor_nbd0.2430.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.3520.3
X-RAY DIFFRACTIONp_planar_tor3.72
X-RAY DIFFRACTIONp_staggered_tor24.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2620
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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