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- PDB-4hrh: Crystal Structure of p11-Annexin A2(N-terminal) Fusion Protein in... -

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Basic information

Entry
Database: PDB / ID: 4hrh
TitleCrystal Structure of p11-Annexin A2(N-terminal) Fusion Protein in Complex with SMARCA3 Peptide
Components
  • Helicase-like transcription factor
  • Protein S100-A10, Annexin A2
KeywordsCalcium-binding protein / EF-hand
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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 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 / ATP-dependent chromatin remodeler activity / 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 / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / ATP-dependent activity, acting on DNA / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / helicase activity / cell-matrix adhesion / positive regulation of GTPase activity / response to activity / protein localization to plasma membrane / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lung development / calcium channel activity / RING-type E3 ubiquitin transferase / 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 / ubiquitin protein ligase activity / melanosome / E3 ubiquitin ligases ubiquitinate target proteins / late endosome membrane / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / transmembrane transporter binding / early endosome / protein ubiquitination / endosome / lysosomal membrane / DNA repair / ubiquitin protein ligase binding / calcium ion binding / Neutrophil degranulation / nucleolus / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein S100-A10 / HIRAN domain / HIRAN domain / HIRAN / Annexin A2 / Zinc finger, C3HC4 type (RING finger) / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin ...Protein S100-A10 / HIRAN domain / HIRAN domain / HIRAN / Annexin A2 / Zinc finger, C3HC4 type (RING finger) / 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 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Helicase conserved C-terminal domain / Zinc finger RING-type profile. / Zinc finger, RING-type / EF-hand domain pair / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Protein S100-A10 / Helicase-like transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsGao, P. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: SMARCA3, a Chromatin-Remodeling Factor, Is Required for p11-Dependent Antidepressant Action.
Authors: Oh, Y.S. / Gao, P. / Lee, K.W. / Ceglia, I. / Seo, J.S. / Zhang, X. / Ahn, J.H. / Chait, B.T. / Patel, D.J. / Kim, Y. / Greengard, P.
History
DepositionOct 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-A10, Annexin A2
B: Protein S100-A10, Annexin A2
C: Helicase-like transcription factor
D: Helicase-like transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6876
Polymers30,4954
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-88 kcal/mol
Surface area11140 Å2
MethodPISA
2
A: Protein S100-A10, Annexin A2
C: Helicase-like transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3443
Polymers15,2472
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-19 kcal/mol
Surface area7860 Å2
MethodPISA
3
B: Protein S100-A10, Annexin A2
D: Helicase-like transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3443
Polymers15,2472
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-18 kcal/mol
Surface area7760 Å2
MethodPISA
4
A: Protein S100-A10, Annexin A2
B: Protein S100-A10, Annexin A2
C: Helicase-like transcription factor
D: Helicase-like transcription factor
hetero molecules

A: Protein S100-A10, Annexin A2
B: Protein S100-A10, Annexin A2
C: Helicase-like transcription factor
D: Helicase-like transcription factor
hetero molecules

A: Protein S100-A10, Annexin A2
B: Protein S100-A10, Annexin A2
C: Helicase-like transcription factor
D: Helicase-like transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,06118
Polymers91,48512
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area24000 Å2
ΔGint-291 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.106, 145.106, 145.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Protein S100-A10, Annexin A2 / 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 / 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: 13441.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ANX2LG, CAL1L, CLP11, S100A10, ANX2, ANX2L4, ANXA2, CAL1H, LPC2D
Production host: Escherichia coli (E. coli) / References: UniProt: P60903, UniProt: P07355
#2: Protein/peptide Helicase-like transcription factor / DNA-binding protein/plasminogen activator inhibitor 1 regulator / HIP116 / RING finger protein 80 / ...DNA-binding protein/plasminogen activator inhibitor 1 regulator / HIP116 / RING finger protein 80 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3 / Sucrose nonfermenting protein 2-like 3


Mass: 1806.069 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human)
References: UniProt: Q14527, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ...References: UniProt: Q14527, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 4.44 Å3/Da / Density % sol: 72.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M MES, 1.6 M (NH4)2SO4, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→29.62 Å / Num. all: 10957 / Num. obs: 10903 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
NECATdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HRG

4hrg


Resolution: 3.001→29.62 Å / SU ML: 0.74 / σ(F): 0 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 549 5.04 %RANDOM
Rwork0.2202 ---
all0.2225 10957 --
obs0.2225 10903 99.5 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.465 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 3.001→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 10 0 1895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091935
X-RAY DIFFRACTIONf_angle_d1.1862585
X-RAY DIFFRACTIONf_dihedral_angle_d19.647719
X-RAY DIFFRACTIONf_chiral_restr0.079273
X-RAY DIFFRACTIONf_plane_restr0.005327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.30260.33981350.29622531X-RAY DIFFRACTION100
3.3026-3.77970.33141240.2282553X-RAY DIFFRACTION100
3.7797-4.75880.21831390.17732580X-RAY DIFFRACTION100
4.7588-29.62110.25581510.23042690X-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)
18.0623-5.9889-0.86289.85852.28194.27110.10080.120.1773-0.011-0.02560.2951-0.1613-0.1999-0.03480.71390.027-0.03070.28990.10680.7051-1.654417.8791-24.928
28.97183.8950.75951.457-4.49342.26041.09160.01450.38110.76-0.1601-0.52780.516-2.8259-0.90471.1814-0.0140.07650.70330.10341.1362-11.729610.0003-14.0163
33.12980.92780.29851.0985-1.50793.84760.6904-4.1931-2.64533.76462.0798-3.8749-0.9036-0.874-1.4921.82410.0464-1.09331.1642-0.0171.81160.529920.4134-9.9634
48.7248-4.33441.48725.3594-0.80814.6154-0.3842-0.0927-1.07920.28940.48931.40930.7701-0.7204-0.02320.683-0.03950.02630.50620.1860.8177-2.54521.4836-20.9456
53.835-4.8695-0.76427.0201-0.97534.00050.14330.0568-0.8274-0.40430.14230.36890.3098-0.0225-0.02630.6939-0.0997-0.16310.3544-0.02870.72013.4650.8111-29.2461
67.16992.1154-0.07723.4478-2.5543.9001-0.38580.4554-0.4756-0.0384-0.2649-2.9896-0.30440.89030.50250.8695-0.09030.02710.628-0.05551.281321.29473.3442-28.3809
72.59130.7932-2.06383.11831.92254.04650.5499-2.4768-2.03134.13440.54663.289-0.95191.294-0.94441.4358-0.093-0.0671.02930.11870.838317.6303-2.4566-16.3945
87.475-2.8401-2.25866.1707-0.42235.589-0.50740.31351.0754-0.330.6834-1.3097-1.0164-0.0347-0.43360.8892-0.15020.0120.5199-0.00170.78912.544316.3965-26.5612
91.93152.34793.39191.79710.94726.031-0.3712-0.67723.26446.50631.0352-1.66330.43390.3904-0.90771.63990.28730.47120.96690.2183-0.07720.53455.092-11.436
102.85934.93251.8252.7511-7.36121.83421.5879-0.72970.27253.24611.0253-3.0593-1.51570.9242-1.38351.3964-0.0818-0.21970.8788-0.08140.99816.865412.3089-17.4502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:37)
2X-RAY DIFFRACTION2chain 'A' and (resseq 38:57)
3X-RAY DIFFRACTION3chain 'A' and (resseq 58:67)
4X-RAY DIFFRACTION4chain 'A' and (resseq 68:113)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:22)
6X-RAY DIFFRACTION6chain 'B' and (resseq 23:57)
7X-RAY DIFFRACTION7chain 'B' and (resseq 58:67)
8X-RAY DIFFRACTION8chain 'B' and (resseq 68:113)
9X-RAY DIFFRACTION9chain 'C'
10X-RAY DIFFRACTION10chain 'D'

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