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- PDB-5lpx: Crystal structure of PKC phosphorylation-mimicking mutant (S26E) ... -

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Basic information

Entry
Database: PDB / ID: 5lpx
TitleCrystal structure of PKC phosphorylation-mimicking mutant (S26E) Annexin A2
ComponentsAnnexin A2
KeywordsCalcium binding protein / protein-protein complex / phospho-mimickation
Function / homology
Function and homology information


positive regulation of low-density lipoprotein particle receptor binding / 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 / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair ...positive regulation of low-density lipoprotein particle receptor binding / 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 / 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 / cornified envelope / vesicle budding from membrane / plasma membrane protein complex / osteoclast development / calcium-dependent phospholipid binding / negative regulation of receptor internalization / 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 / regulation of neurogenesis / basement membrane / Smooth Muscle Contraction / 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 / response to activity / 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 / late endosome membrane / midbody / basolateral plasma membrane / protease binding / angiogenesis / collagen-containing extracellular matrix / vesicle / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / cell surface / 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
Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEcsedi, P. / Gogl, G. / Kiss, B. / Nyitray, L.
CitationJournal: Structure / Year: 2017
Title: Regulation of the Equilibrium between Closed and Open Conformations of Annexin A2 by N-Terminal Phosphorylation and S100A4-Binding.
Authors: Ecsedi, P. / Kiss, B. / Gogl, G. / Radnai, L. / Buday, L. / Koprivanacz, K. / Liliom, K. / Leveles, I. / Vertessy, B. / Jeszenoi, N. / Hetenyi, C. / Schlosser, G. / Katona, G. / Nyitray, L.
History
DepositionAug 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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_symmetry
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0418
Polymers38,6561
Non-polymers3857
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-55 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.950, 58.760, 182.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

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Components

#1: Protein 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: 38655.977 Da / Num. of mol.: 1 / Mutation: S26E, A66E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: P07355
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6, 0.2 M ammonium acetate, 5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.05 Å / Num. obs: 47503 / % possible obs: 99.99 % / Redundancy: 13.18 % / CC1/2: 0.999 / Rsym value: 0.112 / Net I/σ(I): 19.05
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 2.3 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HYW

2hyw


Resolution: 1.9→47.045 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.16
RfactorNum. reflection% reflection
Rfree0.1821 2362 4.98 %
Rwork0.1455 --
obs0.1473 47436 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 17 480 2995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182560
X-RAY DIFFRACTIONf_angle_d1.4693442
X-RAY DIFFRACTIONf_dihedral_angle_d14.4531000
X-RAY DIFFRACTIONf_chiral_restr0.092382
X-RAY DIFFRACTIONf_plane_restr0.007444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93880.27931400.22242577X-RAY DIFFRACTION100
1.9388-1.9810.22811470.21712596X-RAY DIFFRACTION100
1.981-2.02710.231380.18732639X-RAY DIFFRACTION100
2.0271-2.07780.16541380.17452581X-RAY DIFFRACTION100
2.0778-2.13390.21321520.16162603X-RAY DIFFRACTION100
2.1339-2.19670.17621330.14272640X-RAY DIFFRACTION100
2.1967-2.26760.1721540.14112601X-RAY DIFFRACTION100
2.2676-2.34870.16831470.13972628X-RAY DIFFRACTION100
2.3487-2.44270.18951280.14192635X-RAY DIFFRACTION100
2.4427-2.55390.21410.14672618X-RAY DIFFRACTION100
2.5539-2.68850.18431340.14882641X-RAY DIFFRACTION100
2.6885-2.85690.16991130.13932681X-RAY DIFFRACTION100
2.8569-3.07750.18271440.1372662X-RAY DIFFRACTION100
3.0775-3.38710.18221310.14152663X-RAY DIFFRACTION100
3.3871-3.8770.1741380.13232705X-RAY DIFFRACTION100
3.877-4.88380.14981180.12172747X-RAY DIFFRACTION100
4.8838-47.05980.18961660.16192857X-RAY DIFFRACTION100
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)
12.0832-0.33010.11159.668-0.11233.47380.06040.15780.2025-0.27770.02090.0852-0.2891-0.1005-0.10160.42250.0021-0.00620.46270.04350.2342116.6659-29.656369.3726
23.20060.05540.23573.34590.81873.03760.10620.36930.0967-0.3282-0.07510.10450.0448-0.2908-0.02320.33560.0157-0.00860.37650.05340.1856117.5628-32.9935375.1411
30.9484-0.1301-0.32891.75120.6521.9210.0920.0667-0.06710.0316-0.02170.09980.3556-0.5091-0.08450.19-0.0638-0.02110.24790.02130.1753115.0251-36.9518392.1737
42.30140.41971.4921.44021.0924.3483-0.01790.0910.1664-0.0484-0.09880.36030.1648-0.7170.08330.1573-0.00340.03590.3143-0.00690.2443111.3613-26.0815405.5162
52.39511.04170.82442.36310.73312.67530.1695-0.2555-0.03210.3486-0.1144-0.13890.2918-0.1384-0.05950.2469-0.012-0.02140.2255-0.00530.2435127.2245-24.7846419.0404
61.6727-1.99360.02356.80043.13582.26330.0719-0.0837-0.0550.28920.0233-0.20290.1784-0.1346-0.09520.1919-0.0263-0.01660.19640.02880.2118131.577-36.9446399.8604
72.0204-0.27650.6891.71240.02861.99970.09670.18380.082-0.0957-0.0426-0.27720.02010.1869-0.04140.20580.00670.01250.23820.02090.2435132.8578-34.561390.6215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 264 )
6X-RAY DIFFRACTION6chain 'A' and (resid 265 through 284 )
7X-RAY DIFFRACTION7chain 'A' and (resid 285 through 339 )

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