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- PDB-4ftg: The crystal structure of an AHNAK peptide in complex with the S10... -

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Basic information

Entry
Database: PDB / ID: 4ftg
TitleThe crystal structure of an AHNAK peptide in complex with the S100A10/AnxA2 heterotetramer
Components
  • Annexin A2
  • Neuroblast differentiation-associated protein AHNAK
  • Protein S100-A10
KeywordsCALCIUM-BINDING PROTEIN/PROTEIN BINDING / Membrane repair / scaffold / AHNAK / Annexin A2 / S100A10 / calcium binding / inner-membrane surface / CALCIUM BINDING PROTEIN-PROTEIN BINDING complex / CALCIUM-BINDING PROTEIN-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 / PCSK9-AnxA2 complex / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / structural molecule activity conferring elasticity ...regulation of voltage-gated calcium channel activity / positive regulation of low-density lipoprotein particle receptor binding / PCSK9-AnxA2 complex / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / 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 / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / cornified envelope / cell-cell contact zone / vesicle budding from membrane / negative regulation of receptor internalization / plasma membrane protein complex / costamere / osteoclast development / calcium-dependent phospholipid binding / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / positive regulation of low-density lipoprotein receptor activity / 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 / regulation of neurogenesis / basement membrane / Smooth Muscle Contraction / positive regulation of substrate adhesion-dependent cell spreading / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of stress fiber assembly / fibrinolysis / cytoskeletal protein binding / T-tubule / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cell-matrix adhesion / lipid droplet / positive regulation of GTPase activity / response to activity / protein localization to plasma membrane / adherens junction / lung development / 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 / protease binding / angiogenesis / collagen-containing extracellular matrix / 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 / cytosol / cytoplasm
Similarity search - Function
: / Protein S100-A10 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily ...: / 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
ISOPROPYL ALCOHOL / Annexin A2 / Protein S100-A10 / Neuroblast differentiation-associated protein AHNAK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5054 Å
AuthorsOzorowski, G. / Luecke, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of a C-terminal AHNAK peptide in a 1:2:2 complex with S100A10 and an acetylated N-terminal peptide of annexin A2.
Authors: Ozorowski, G. / Milton, S. / Luecke, H.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A10
B: Protein S100-A10
C: Annexin A2
D: Annexin A2
E: Neuroblast differentiation-associated protein AHNAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0078
Polymers27,8265
Non-polymers1803
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-81 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.072, 55.216, 63.140
Angle α, β, γ (deg.)90.00, 111.73, 90.00
Int Tables number5
Space group name H-MC121
DetailsOne AHNAK peptide bound to AnxA2/S100A10 heterotetramer, formed by a dimer of S100A10 binding two AnxA2 N-terminal peptides

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Components

#1: Protein Protein S100-A10 / 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: 11088.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANX2LG, CAL1L, CLP11, S100A10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60903
#2: Protein/peptide Annexin A2 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / ...Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 1653.854 Da / Num. of mol.: 2 / Fragment: Annexin A2 N-terminal peptide (UNP residues 2-16) / Mutation: C9S / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07355
#3: Protein/peptide Neuroblast differentiation-associated protein AHNAK / Desmoyokin


Mass: 2340.870 Da / Num. of mol.: 1 / Fragment: AHNAK peptide (UNP residues 5654-5673) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q09666
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 8000 (w/v), 0.1 M Tris pH 8.5, 10% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8685 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.543.10.42196.9
2.54-2.593.30.353198.6
2.59-2.643.50.347197.8
2.64-2.693.60.273199.3
2.69-2.753.70.221198.6
2.75-2.823.80.188198.6
2.82-2.893.80.167199.3
2.89-2.963.80.155198.6
2.96-3.053.80.134198.6
3.05-3.153.80.123199.3
3.15-3.263.80.091198.6
3.26-3.393.80.082198.9
3.39-3.553.80.074198.6
3.55-3.733.70.068198.7
3.73-3.973.70.065198.7
3.97-4.273.70.055199.3
4.27-4.73.60.054199.1
4.7-5.383.60.055199.1
5.38-6.783.60.044198.7
6.78-503.50.033195.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5054→29.327 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.36 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 415 4.79 %
Rwork0.1813 --
obs0.1846 8670 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.3688 Å2
Refinement stepCycle: LAST / Resolution: 2.5054→29.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 12 8 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091842
X-RAY DIFFRACTIONf_angle_d1.2232446
X-RAY DIFFRACTIONf_dihedral_angle_d14.76686
X-RAY DIFFRACTIONf_chiral_restr0.091266
X-RAY DIFFRACTIONf_plane_restr0.005304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5054-2.86760.27291500.17952703X-RAY DIFFRACTION98
2.8676-3.61190.27251240.21022755X-RAY DIFFRACTION99
3.6119-29.32880.23631410.1692797X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7510.4777-0.75410.8162-0.73621.7984-0.14740.0472-0.54390.1923-0.0422-0.15180.1132-0.11290.00030.29550.0580.01260.1968-0.03780.3569.79120.744848.3782
21.53490.2305-0.26231.0832-0.71290.9242-0.26990.65190.08270.0620.19710.0784-0.5334-0.5756-0.01850.37380.2531-0.00630.42470.00550.233258.414634.520341.2357
30.55530.4968-0.14730.5757-0.28340.2159-0.00320.14840.3068-0.18570.16110.28230.2278-0.02150.16970.1695-0.1566-0.23410.9748-0.1160.378552.701925.078933.3291
40.02180.09680.03180.38570.11730.03610.0323-0.08340.05860.3390.0441-0.3890.00710.2641-0.00120.2425-0.0895-0.07930.50810.00530.410579.755329.232449.4202
50.25230.0283-0.19910.4748-0.2730.32050.13940.1477-0.65220.3589-0.06550.08630.1517-0.0622-0.00080.5880.03750.1580.7911-0.03850.446958.69427.058350.8682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:91)
2X-RAY DIFFRACTION2(chain B and resid 1:91)
3X-RAY DIFFRACTION3(chain C and resid 2:13)
4X-RAY DIFFRACTION4(chain D and resid 2:14)
5X-RAY DIFFRACTION5(chain E and resid 1:16)

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