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- PDB-1qls: S100C (S100A11),OR CALGIZZARIN, IN COMPLEX WITH ANNEXIN I N-TERMINUS -

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Basic information

Entry
Database: PDB / ID: 1qls
TitleS100C (S100A11),OR CALGIZZARIN, IN COMPLEX WITH ANNEXIN I N-TERMINUS
Components
  • ANNEXIN I
  • S100C PROTEIN
KeywordsMETAL-BINDING PROTEIN/INHIBITOR / S100 FAMILY / EF-HAND PROTEIN / COMPLEX (LIGAND-ANNEXIN) / LIGAND OF ANNEXIN II / CALCIUM/PHOSPHOLIPID BINDING PROTEIN / METAL-BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of interleukin-1 production / myoblast migration involved in skeletal muscle regeneration / granulocyte chemotaxis / regulation of leukocyte migration / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / regulation of hormone secretion / positive regulation of vesicle fusion / neutrophil clearance / positive regulation of neutrophil apoptotic process ...regulation of interleukin-1 production / myoblast migration involved in skeletal muscle regeneration / granulocyte chemotaxis / regulation of leukocyte migration / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / regulation of hormone secretion / positive regulation of vesicle fusion / neutrophil clearance / positive regulation of neutrophil apoptotic process / cadherin binding involved in cell-cell adhesion / peptide cross-linking / negative regulation of interleukin-8 production / cornified envelope / neutrophil activation / Neutrophil degranulation / neutrophil homeostasis / calcium-dependent phospholipid binding / negative regulation of T-helper 2 cell differentiation / S100 protein binding / Formyl peptide receptors bind formyl peptides and many other ligands / negative regulation of exocytosis / vesicle membrane / alpha-beta T cell differentiation / cellular response to glucocorticoid stimulus / motile cilium / positive regulation of cell migration involved in sprouting angiogenesis / arachidonate secretion / positive regulation of wound healing / phosphatidylserine binding / monocyte chemotaxis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / Smooth Muscle Contraction / cellular response to vascular endothelial growth factor stimulus / phagocytic cup / positive regulation of G1/S transition of mitotic cell cycle / lateral plasma membrane / phagocytosis / positive regulation of T cell proliferation / keratinocyte differentiation / positive regulation of interleukin-2 production / adherens junction / sarcolemma / phospholipid binding / calcium-dependent protein binding / regulation of cell shape / regulation of cell population proliferation / actin cytoskeleton organization / regulation of inflammatory response / early endosome membrane / : / G alpha (i) signalling events / Interleukin-4 and Interleukin-13 signaling / basolateral plasma membrane / G alpha (q) signalling events / vesicle / adaptive immune response / cell surface receptor signaling pathway / endosome / apical plasma membrane / inflammatory response / signaling receptor binding / innate immune response / focal adhesion / lipid binding / calcium ion binding / negative regulation of apoptotic process / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein S100-A11 / Annexin A1 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Protein S100-A11 / Annexin A1 / 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 domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Annexin A1 / Protein S100-A11
Similarity search - Component
Biological speciesSUS SCROFA (pig)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRety, S. / Sopkova, J. / Renouard, M. / Osterloh, D. / Gerke, V. / Russo-Marie, F. / Lewit-Bentley, A.
CitationJournal: Structure / Year: 2000
Title: Structural Basis of the Ca2+ Dependent Association between S100C (S100A11) and its Target, the N-Terminal Part of Annexin I
Authors: Rety, S. / Osterloh, D. / Arie, J.P. / Tabaries, S. / Seeman, J. / Russo-Marie, F. / Gerke, V. / Lewit-Bentley, A.
History
DepositionSep 15, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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 / _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.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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 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.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S100C PROTEIN
D: ANNEXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5544
Polymers12,4732
Non-polymers802
Water41423
1
A: S100C PROTEIN
D: ANNEXIN I
hetero molecules

A: S100C PROTEIN
D: ANNEXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1078
Polymers24,9474
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
Buried area5820 Å2
ΔGint-59.1 kcal/mol
Surface area12460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.510, 77.510, 111.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsBIOLOGICAL_UNIT: DIMERTHE DIMER IS COVALENT IN THE CRYSTAL, LINKED BY ADISULPHIDE AT CYS11. UNDER REDUCING CONDITIONS, THOUGHTHE DISULPHIDE WOULD BE REDUCED, THE DIMER SHOULD REMAININTACT.FOR THE HOMO-ASSEMBLY DESCRIBED BY REMARK 350THE DIFFERENCE IN ACCESSIBLE SURFACE AREA PERCHAIN BETWEEN THE ISOLATED CHAIN AND THAT FOR

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Components

#1: Protein S100C PROTEIN / CALGIZZARIN


Mass: 11194.829 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P31950
#2: Protein/peptide ANNEXIN I


Mass: 1278.541 Da / Num. of mol.: 1 / Fragment: N-TERMINAL / Source method: obtained synthetically / Details: N-ACETYLATED ON N-TERMINUS / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P04083
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSYNTHETIC ANNEXIN I N-TERMINAL SEQUENCE

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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: 3.9 Å3/Da / Density % sol: 68.2 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: 20 MG/ML PROTEIN WERE CRYSTALLIZED BY VAPOR DIFFUSION AGAINST 10% PEG 4000, 20% PEG 4000, 10% 2-PROPANOL, 100MM HEPES, PH=8.5, pH 8.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of 1:1 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 %PEG40001reservoir
310 %2-propanol1reservoir
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.37
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 2, 1998 / Details: FOCUSSING MONOCHROMATOR
RadiationMonochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 2.3→69 Å / Num. obs: 9310 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 20.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 61772

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BT6

1bt6


Resolution: 2.3→20 Å / SU B: 4.869 / SU ML: 0.1216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.207
RfactorNum. reflection% reflectionSelection details
Rfree0.268 930 10 %RANDOM
Rwork0.214 ---
obs-9333 99.7 %-
Displacement parametersBiso mean: 200.109 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 2 23 865
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4172
X-RAY DIFFRACTIONp_mcangle_it3.3573
X-RAY DIFFRACTIONp_scbond_it4.483
X-RAY DIFFRACTIONp_scangle_it6.6024
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.2030.15
X-RAY DIFFRACTIONp_singtor_nbd0.2060.3
X-RAY DIFFRACTIONp_multtor_nbd0.350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.3
X-RAY DIFFRACTIONp_planar_tor2.115
X-RAY DIFFRACTIONp_staggered_tor2315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.820
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_deg1.6

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