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- PDB-5lpu: Crystal structure of Annexin A2 complexed with S100A4 -

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Basic information

Entry
Database: PDB / ID: 5lpu
TitleCrystal structure of Annexin A2 complexed with S100A4
Components
  • Annexin A2
  • Protein S100-A4
Keywordscalcium-binding protein / protein-protein complex
Function / homology
Function and homology information


: / 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 ...: / 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 / RAGE receptor binding / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / cornified envelope / vesicle budding from membrane / osteoclast development / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / : / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / chemoattractant activity / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / transition metal ion binding / Smooth Muscle Contraction / epithelial to mesenchymal transition / cytoskeletal protein binding / fibrinolysis / lipid droplet / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / response to activity / adherens junction / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / actin binding / midbody / protease binding / : / basolateral plasma membrane / angiogenesis / vesicle / positive regulation of canonical NF-kappaB signal transduction / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
S-100 / Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily ...S-100 / Annexin A2 / Annexin / 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 / Annexin V; domain 1 / 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 A2 / Protein S100-A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / struct_conn_type
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_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.ptnr2_symmetry / _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.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Protein S100-A4
D: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,30523
Polymers101,2844
Non-polymers1,02219
Water5,188288
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-222 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.740, 61.240, 148.160
Angle α, β, γ (deg.)90.00, 88.69, 90.00
Int Tables number4
Space group name H-MP1211

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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: 38613.941 Da / Num. of mol.: 2 / Mutation: 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: Protein Protein S100-A4 / Calvasculin / Metastasin / Placental calcium-binding protein / Protein Mts1 / S100 calcium-binding protein A4


Mass: 12027.813 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A4, CAPL, MTS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P26447
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis Tris pH 6.5, 0.2M ammonium acetate 4% PEG4000 and 1,5% glycerol

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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: 2.1→49.374 Å / Num. obs: 75455 / % possible obs: 99.98 % / Redundancy: 13.6 % / Rsym value: 0.067 / Net I/σ(I): 23.1
Reflection shellResolution: 2.1→2.17 Å / Mean I/σ(I) obs: 2.42 / % possible all: 99.87

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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: 2.1→49.374 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.03
RfactorNum. reflection% reflection
Rfree0.2073 3752 4.98 %
Rwork0.1808 --
obs0.1821 75380 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6781 0 44 288 7113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046935
X-RAY DIFFRACTIONf_angle_d0.6839341
X-RAY DIFFRACTIONf_dihedral_angle_d12.2482623
X-RAY DIFFRACTIONf_chiral_restr0.0261042
X-RAY DIFFRACTIONf_plane_restr0.0031211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12660.33161330.28452620X-RAY DIFFRACTION100
2.1266-2.15460.33811470.26132616X-RAY DIFFRACTION100
2.1546-2.18410.27181400.25042667X-RAY DIFFRACTION100
2.1841-2.21530.26291430.24492604X-RAY DIFFRACTION100
2.2153-2.24840.25641680.23582608X-RAY DIFFRACTION100
2.2484-2.28350.27581190.22832617X-RAY DIFFRACTION100
2.2835-2.32090.22441260.21512657X-RAY DIFFRACTION100
2.3209-2.36090.21721600.19562644X-RAY DIFFRACTION100
2.3609-2.40390.21211370.2022636X-RAY DIFFRACTION100
2.4039-2.45010.21951500.20652603X-RAY DIFFRACTION100
2.4501-2.50010.221490.20122612X-RAY DIFFRACTION100
2.5001-2.55450.24721370.19762721X-RAY DIFFRACTION100
2.5545-2.61390.26061340.20522569X-RAY DIFFRACTION100
2.6139-2.67930.24271340.21432685X-RAY DIFFRACTION100
2.6793-2.75170.23571210.20152643X-RAY DIFFRACTION100
2.7517-2.83270.22011390.20632636X-RAY DIFFRACTION100
2.8327-2.92410.23971270.20342657X-RAY DIFFRACTION100
2.9241-3.02860.20521550.2042640X-RAY DIFFRACTION100
3.0286-3.14980.18811150.19832692X-RAY DIFFRACTION100
3.1498-3.29310.19551360.19622641X-RAY DIFFRACTION100
3.2931-3.46670.2021420.20332667X-RAY DIFFRACTION100
3.4667-3.68390.23761520.19122622X-RAY DIFFRACTION100
3.6839-3.96820.21781570.17012676X-RAY DIFFRACTION100
3.9682-4.36730.16031440.14392674X-RAY DIFFRACTION100
4.3673-4.99870.17851180.14692710X-RAY DIFFRACTION100
4.9987-6.29580.20371390.17612712X-RAY DIFFRACTION100
6.2958-49.38730.16541300.13752799X-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)
14.8208-6.3156-0.97498.26221.28980.147-0.82160.4164-1.45871.0646-0.50830.57880.3298-1.05061.47270.6468-0.07880.11111.1816-0.01551.02771.0368-16.0724199.3665
22.3767-0.1433-0.62461.3737-0.54511.81420.22940.21060.0139-0.1522-0.25540.02530.00420.1520.04080.290.03610.00420.2552-0.04450.3764-14.09492.4591213.9422
38.0214.5026-0.05797.5788-5.01174.6623-0.0374-0.6498-0.6362-0.3585-0.4149-0.98560.45151.15410.60920.42010.16730.04670.42020.01660.508628.7288-18.7998193.8324
43.11110.7437-1.02691.96440.6492.91490.40390.40110.403-0.4271-0.24440.0947-0.548-0.2723-0.17940.9250.27130.36841.02070.21750.727244.55041.048162.8765
52.37290.0122-0.58522.00560.89830.72560.19790.4727-0.0222-0.50260.001-0.2356-0.4551-0.1514-0.21390.98750.16090.38530.95180.1950.709262.7366-6.1118146.6259
65.29333.06993.25044.86655.00575.0496-0.15920.9435-0.0149-1.14890.2642-0.1191-1.28410.1726-0.05790.63220.13530.07320.70650.12730.378921.0659-6.1841185.5906
73.04815.301-0.51069.5032-2.47659.56960.03170.210.95220.14-0.25190.1294-1.8105-0.32140.2660.69570.0928-0.02730.56550.04570.608126.68181.2751199.1022
89.79752.1275-1.72526.6596-0.28798.19280.16920.20830.3460.5647-0.02720.9524-0.6591-0.9267-0.15990.44760.17750.09290.56620.02740.430414.4461-5.3386199.5031
99.9753-6.4716.8654.4351-5.07486.3709-0.4692-1.04160.13741.13820.0721.5471-0.6018-1.50230.41471.0860.25960.341.06820.03651.23567.0467-9.4744207.2581
108.02476.7351-5.94146.5422-5.53334.72460.2947-0.88140.01640.9859-0.2094-0.3493-0.07161.2546-0.11110.57440.0362-0.08860.6203-0.00580.384625.0088-10.1233206.3616
117.52014.9310.87063.29321.15082.1236-0.147-0.1745-0.5819-0.0574-0.1263-0.12010.2896-0.19920.190.53540.07660.0580.54430.03270.492619.7369-18.3951193.6254
128.69553.59745.71533.119-0.50778.6919-0.21620.7952-0.5862-0.96780.34161.20760.356-0.8742-0.07830.5708-0.08850.00040.8441-0.10720.550113.127-16.2794184.3071
133.34-1.18152.94489.55452.16663.8436-0.30821.3656-0.9487-0.44630.1907-0.321.4863-0.34830.21441.1801-0.02120.32241.0219-0.30230.749526.1219-23.4308174.8053
147.4554-1.4457-1.98080.55761.68217.5153-0.29850.4599-1.4751-0.8569-0.2011-1.00740.88220.58420.36750.6620.2280.26750.7465-0.01670.82131.2804-19.7889184.355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 339 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 32 )
4X-RAY DIFFRACTION4chain 'B' and (resid 33 through 136 )
5X-RAY DIFFRACTION5chain 'B' and (resid 137 through 339 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 20 )
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 30 )
8X-RAY DIFFRACTION8chain 'C' and (resid 31 through 46 )
9X-RAY DIFFRACTION9chain 'C' and (resid 47 through 51 )
10X-RAY DIFFRACTION10chain 'C' and (resid 52 through 71 )
11X-RAY DIFFRACTION11chain 'C' and (resid 72 through 91 )
12X-RAY DIFFRACTION12chain 'D' and (resid -1 through 20 )
13X-RAY DIFFRACTION13chain 'D' and (resid 21 through 51 )
14X-RAY DIFFRACTION14chain 'D' and (resid 52 through 93 )

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