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- PDB-5lq0: Crystal structure of Tyr24 phosphorylated Annexin A2 at 2.9 A res... -

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Basic information

Entry
Database: PDB / ID: 5lq0
TitleCrystal structure of Tyr24 phosphorylated Annexin A2 at 2.9 A resolution
ComponentsAnnexin A2
Keywordscalcium binding protein / tyrosine phosphorylation
Function / homology
Function and homology information


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 / 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 / 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 / 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 / plasma membrane protein complex / 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 / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein 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 / 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 / late endosome membrane / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / 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: 2.9 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 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Annexin A2
B: Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6288
Polymers77,3882
Non-polymers2406
Water1267
1
A: Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8144
Polymers38,6941
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8144
Polymers38,6941
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.450, 63.470, 268.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 38693.918 Da / Num. of mol.: 2 / Mutation: A66E Y24(PTR)
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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6, 0.1 M magnesium chloride, 4% PEG6000

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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: 2.9→47.77 Å / Num. obs: 22187 / % possible obs: 99.12 % / Redundancy: 9.14 % / CC1/2: 0.999 / Rsym value: 0.094 / Net I/σ(I): 18.67
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.33 % / Mean I/σ(I) obs: 3.22 / % possible all: 99.86

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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: 2.9→47.767 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.91
RfactorNum. reflection% reflection
Rfree0.2598 1102 4.98 %
Rwork0.2265 --
obs0.2282 22125 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 6 7 5017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025077
X-RAY DIFFRACTIONf_angle_d0.6276844
X-RAY DIFFRACTIONf_dihedral_angle_d12.6451931
X-RAY DIFFRACTIONf_chiral_restr0.023767
X-RAY DIFFRACTIONf_plane_restr0.002884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.03210.40681460.32812602X-RAY DIFFRACTION100
3.0321-3.19190.34111420.28452556X-RAY DIFFRACTION100
3.1919-3.39180.34991160.27412646X-RAY DIFFRACTION100
3.3918-3.65360.31361250.29492510X-RAY DIFFRACTION96
3.6536-4.02110.35121270.2712575X-RAY DIFFRACTION97
4.0211-4.60260.23391550.18482611X-RAY DIFFRACTION100
4.6026-5.79720.20831380.18752693X-RAY DIFFRACTION100
5.7972-47.77340.17711530.17712830X-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)
14.9113-0.1454-2.12241.764-0.8086.5380.0232-0.1852-0.0793-0.0551-0.20960.019-0.5165-0.04850.22750.49180.06060.00850.3495-0.06480.3199-16.832114.859-32.007
20.7951-0.677-0.74451.96060.53473.07760.09110.2749-0.1771-0.613-0.43660.4236-0.5119-0.64490.3130.5330.1309-0.14070.5657-0.1470.4688-16.06679.3687-65.3921
33.3850.7591-2.61244.09911.24613.94920.0809-0.1557-0.0076-0.16360.022-0.3061-0.28280.001-0.0870.48780.0549-0.08330.43680.03460.2482-3.169218.7765-48.8972
41.7654-0.1284-1.56292.48470.3284.8722-0.0245-0.34630.06220.0386-0.0585-0.317-0.40310.22390.06030.2687-0.0153-0.01020.3742-0.00340.4937-23.886514.90577.1291
53.97123.75591.72326.8391-0.23592.9179-0.47160.6166-0.5871-0.39890.4720.15650.1809-0.6177-0.09830.3524-0.08750.06270.3838-0.01060.4829-32.71120.364-13.0143
61.40280.61750.53332.64080.51283.0025-0.1791-0.0469-0.5721-0.17310.0036-0.35620.4482-0.01540.10940.32280.03440.17210.41320.07410.8084-26.0607-8.8129-3.3216
73.8239-1.56321.53134.71592.48557.94570.9693-1.1397-0.37960.6052-0.83840.05560.31260.0077-0.31320.41720.0182-0.10920.57510.19630.5639-20.59632.369819.3676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 21 through 92 )
2X-RAY DIFFRACTION2chain 'B' and (resid 93 through 276 )
3X-RAY DIFFRACTION3chain 'B' and (resid 277 through 339 )
4X-RAY DIFFRACTION4chain 'A' and (resid 23 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 187 )
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 324 )
7X-RAY DIFFRACTION7chain 'A' and (resid 325 through 339 )

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