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- PDB-4drw: Crystal Structure of the Ternary Complex between S100A10, an Anne... -

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Basic information

Entry
Database: PDB / ID: 4drw
TitleCrystal Structure of the Ternary Complex between S100A10, an Annexin A2 N-terminal Peptide and an AHNAK Peptide
Components
  • Neuroblast differentiation-associated protein AHNAK
  • Protein S100-A10/Annexin A2 chimeric protein
KeywordsEXOCYTOSIS/PROTEIN BINDING / ATYPICAL EF-HAND / HETEROPENTAMERIC COMPLEX / MEMBRANE REPAIR / EXOCYTOSIS-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of voltage-gated calcium channel activity / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / structural molecule activity conferring elasticity / positive regulation of vesicle fusion ...regulation of voltage-gated calcium channel activity / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / structural molecule activity conferring elasticity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / cell-cell contact zone / plasma membrane protein complex / costamere / calcium-dependent phospholipid binding / negative regulation of receptor internalization / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / virion binding / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / positive regulation of focal adhesion assembly / regulation of RNA splicing / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / T-tubule / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / positive regulation of GTPase activity / response to activity / protein localization to plasma membrane / adherens junction / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / actin cytoskeleton / late endosome membrane / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / transmembrane transporter binding / early endosome / endosome / cadherin binding / lysosomal membrane / focal adhesion / calcium ion binding / Neutrophil degranulation / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Protein S100-A10 / Neuroblast differentiation-associated protein AHNAK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRezvanpour, A. / Lee, T.-W. / Junop, M.S. / Shaw, G.S.
CitationJournal: Structure / Year: 2012
Title: Structure of an asymmetric ternary protein complex provides insight for membrane interaction.
Authors: Dempsey, B.R. / Rezvanpour, A. / Lee, T.W. / Barber, K.R. / Junop, M.S. / Shaw, G.S.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-A10/Annexin A2 chimeric protein
B: Protein S100-A10/Annexin A2 chimeric protein
C: Protein S100-A10/Annexin A2 chimeric protein
D: Protein S100-A10/Annexin A2 chimeric protein
E: Neuroblast differentiation-associated protein AHNAK
F: Neuroblast differentiation-associated protein AHNAK


Theoretical massNumber of molelcules
Total (without water)59,6976
Polymers59,6976
Non-polymers00
Water00
1
A: Protein S100-A10/Annexin A2 chimeric protein
B: Protein S100-A10/Annexin A2 chimeric protein
E: Neuroblast differentiation-associated protein AHNAK


Theoretical massNumber of molelcules
Total (without water)29,8483
Polymers29,8483
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-50 kcal/mol
Surface area11540 Å2
MethodPISA
2
C: Protein S100-A10/Annexin A2 chimeric protein
D: Protein S100-A10/Annexin A2 chimeric protein
F: Neuroblast differentiation-associated protein AHNAK


Theoretical massNumber of molelcules
Total (without water)29,8483
Polymers29,8483
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-52 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.755, 47.791, 62.817
Angle α, β, γ (deg.)71.62, 71.63, 68.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein S100-A10/Annexin A2 chimeric protein / Calpactin I light chain / Calpactin-1 light chain / Cellular ligand of annexin II / S100 calcium- ...Calpactin I light chain / Calpactin-1 light chain / Cellular ligand of annexin II / S100 calcium-binding protein A10 / p10 protein / p11


Mass: 13765.778 Da / Num. of mol.: 4
Fragment: UNP P60903 residues 1-93 and UNP P07355 residues 2-16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A10, ANX2LG, CAL1L, CLP11 / Production host: Escherichia coli (E. coli) / References: UniProt: P60903, UniProt: P07355
#2: Protein/peptide Neuroblast differentiation-associated protein AHNAK / Desmoyokin


Mass: 2316.824 Da / Num. of mol.: 2 / Fragment: UNP Q09666 residues 5654-5673 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED BASED ON HUMAN SEQUENCE / Source: (synth.) Homo sapiens (human) / References: UniProt: Q09666

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM sodium chloride, 200mM magnesium chloride, 50mM sodium cacodylate, 20% PEG 1000, 0.15mM CYMAL-7, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2010
RadiationMonochromator: DOUBLE Si(111) CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.26→43.34 Å / Num. all: 7410 / Num. obs: 7306 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.26→3.32 Å / % possible all: 100

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Processing

Software
NameClassification
CBASSdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BT6

1bt6


Resolution: 3.5→43.34 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.327 605 RANDOM
Rwork0.296 --
all0.35 5817 -
obs0.322 5517 -
Refinement stepCycle: LAST / Resolution: 3.5→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 0 0 3490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.165
X-RAY DIFFRACTIONc_bond_d0.014

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