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

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Basic information

Entry
Database: PDB / ID: 4hrg
TitleCrystal Structure of p11-Annexin A2(N-terminal) Fusion Protein in Complex with AHNAK1 Peptide
Components
  • Neuroblast differentiation-associated protein AHNAK
  • Protein S100-A10
KeywordsCalcium-binding protein / EF-hand
Function / homology
Function and homology information


regulation of voltage-gated calcium channel activity / AnxA2-p11 complex / membrane raft assembly / structural molecule activity conferring elasticity / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / vesicle budding from membrane / cell-cell contact zone / plasma membrane protein complex / costamere ...regulation of voltage-gated calcium channel activity / AnxA2-p11 complex / membrane raft assembly / structural molecule activity conferring elasticity / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / vesicle budding from membrane / cell-cell contact zone / plasma membrane protein complex / costamere / Dissolution of Fibrin Clot / S100 protein binding / positive regulation of exocytosis / positive regulation of focal adhesion assembly / regulation of RNA splicing / regulation of neurogenesis / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / T-tubule / positive regulation of GTPase activity / protein localization to plasma membrane / mRNA transcription by RNA polymerase II / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / actin cytoskeleton / collagen-containing extracellular matrix / vesicle / transmembrane transporter binding / cadherin binding / lysosomal membrane / focal adhesion / calcium ion binding / 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 / cytoplasm / cytosol
Similarity search - Function
Protein S100-A10 / 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. ...Protein S100-A10 / 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
Protein S100-A10 / Neuroblast differentiation-associated protein AHNAK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0001 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 1.1Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Neuroblast differentiation-associated protein AHNAK
D: Neuroblast differentiation-associated protein AHNAK


Theoretical massNumber of molelcules
Total (without water)30,2274
Polymers30,2274
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-72 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.278, 55.645, 60.616
Angle α, β, γ (deg.)90.00, 105.98, 90.00
Int Tables number4
Space group name H-MP1211

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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: 13269.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A10, ANX2LG, CAL1L, CLP11 / Production host: Escherichia coli (E. coli) / References: UniProt: P60903
#2: Protein/peptide Neuroblast differentiation-associated protein AHNAK / Desmoyokin


Mass: 1844.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q09666
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Tris, 30 % PEG 6000, pH 7.4, 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: 2→15 Å / Num. all: 20104 / Num. obs: 20094 / % possible obs: 99.95 % / 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 1BT6

1bt6


Resolution: 2.0001→14.99 Å / SU ML: 0.49 / σ(F): 2 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 988 4.92 %RANDOM
Rwork0.1908 ---
obs0.1921 20094 99.95 %-
all-20104 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.742 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.6869 Å2-0 Å2-4.3946 Å2
2---5.8684 Å2-0 Å2
3----6.8185 Å2
Refinement stepCycle: LAST / Resolution: 2.0001→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 0 129 2101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132006
X-RAY DIFFRACTIONf_angle_d1.5112680
X-RAY DIFFRACTIONf_dihedral_angle_d17.284754
X-RAY DIFFRACTIONf_chiral_restr0.105287
X-RAY DIFFRACTIONf_plane_restr0.006339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10520.24971450.23242692X-RAY DIFFRACTION100
2.1052-2.23670.21671590.19592676X-RAY DIFFRACTION100
2.2367-2.40880.21051320.18732750X-RAY DIFFRACTION100
2.4088-2.650.21891500.19482710X-RAY DIFFRACTION100
2.65-3.03070.22331190.19972744X-RAY DIFFRACTION100
3.0307-3.8080.21321440.19012740X-RAY DIFFRACTION100
3.808-14.990.21341390.17962794X-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)
12.0471-0.45190.68489.53163.40666.46150.0178-0.1933-0.30520.18640.15370.3030.6045-0.2067-0.14240.1809-0.03070.00360.19010.05640.2044-17.1173-1.3885-7.0701
22.2092-5.8574-3.3552.28132.90519.22140.24210.6387-0.8639-0.2542-0.22790.93211.1769-0.8284-0.14160.4221-0.1176-0.07920.2528-0.02230.4178-20.6435-6.064-19.7605
36.1707-0.3084-6.07449.4509-1.41562.03380.34631.1159-0.4402-0.7376-0.12591.1467-0.4444-1.7587-0.2720.39250.0886-0.13870.4179-0.03340.3564-24.86351.36-24.5681
42.24-4.0609-0.08592.2788-1.1382.31060.10050.52140.068-0.9313-0.28370.2875-0.77090.41740.39650.51570.0405-0.05790.4321-0.08490.3055-15.1474-2.1646-29.3196
58.19611.28340.00167.3484-2.49236.2823-0.48941.595-0.526-0.28350.4745-1.3080.24641.21410.41940.60190.07040.02610.6368-0.1210.4232-5.6123-5.315-18.6903
64.1631-2.67971.70863.1586-4.15435.7949-0.10270.09850.02230.01980.079-0.1005-0.1779-0.0359-0.04120.1995-0.0124-0.00860.1515-0.03020.1871-15.678310.3949-18.5285
77.0434-3.7484-4.38942.946545.19871.28390.36410.74910.4587-0.2661.0925-0.493-1.2295-0.23780.4510.16110.00150.26530.1250.5803-28.854420.9749-16.2315
82.31991.62-1.11012.81961.92522.5718-0.07170.60470.2299-0.9292-0.00590.0387-0.3244-0.45910.43570.34120.0238-0.03710.33910.01830.328-22.96889.7452-24.5594
96.75132.92992.64432.94611.81466.0581-0.12740.07670.53570.1990.00830.3944-0.6096-0.32440.15370.22570.07750.00620.1852-0.00470.2313-19.616416.6977-10.9714
105.58390.39292.67486.3207-3.87427.6178-0.098-0.68020.55411.0527-0.1674-0.0407-1.3104-0.26590.25180.50020.0423-0.06730.2498-0.07040.2504-11.206118.8021.7789
119.71431.3115.658.3521-0.84356.92660.03520.86550.2471-0.4041-0.087-0.1409-0.22551.2228-0.12750.275-0.0441-0.07410.3555-0.05430.3894-1.892719.4555-5.1825
123.7116-3.29622.95352.9421-4.00327.484-0.0586-0.03440.051-0.0651-0.0705-0.2492-0.00920.22730.0630.1366-0.01250.01350.1727-0.02060.1906-8.98255.3978-5.6911
13-0.04290.5029-0.0148.9039-2.47060.70462.08530.8449-4.32051.0230.4979-0.18883.37921.4259-0.3837-0.0286-0.62181.2853-0.071.18-0.9439-16.1445-6.47485.9941
1410.0192.67942.09142.6726-1.29262.4886-0.072-0.3432-0.24630.37240.0593-0.630.06510.30650.13650.3516-0.0006-0.00640.2779-0.01140.2768-8.30965.83763.7385
153.4675-2.47413.09862.6805-2.80043.95480.14690.01430.4554-0.2384-0.1713-0.6752-0.60361.1212-0.01630.8004-0.13660.13760.601-0.03080.302-11.07098.5778-23.9832
164.92392.1407-2.68932.1848-9.70392.0436-0.26261.06410.0699-1.0078-0.2622-1.27141.51520.38340.9570.5091-0.01210.06270.488-0.01730.5691-1.90097.4842-6.342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:26)
2X-RAY DIFFRACTION2chain 'A' and (resseq 27:37)
3X-RAY DIFFRACTION3chain 'A' and (resseq 38:44)
4X-RAY DIFFRACTION4chain 'A' and (resseq 45:57)
5X-RAY DIFFRACTION5chain 'A' and (resseq 58:67)
6X-RAY DIFFRACTION6chain 'A' and (resseq 68:89)
7X-RAY DIFFRACTION7chain 'A' and (resseq 90:101)
8X-RAY DIFFRACTION8chain 'A' and (resseq 102:113)
9X-RAY DIFFRACTION9chain 'B' and (resseq 1:26)
10X-RAY DIFFRACTION10chain 'B' and (resseq 27:44)
11X-RAY DIFFRACTION11chain 'B' and (resseq 45:67)
12X-RAY DIFFRACTION12chain 'B' and (resseq 68:89)
13X-RAY DIFFRACTION13chain 'B' and (resseq 90:101)
14X-RAY DIFFRACTION14chain 'B' and (resseq 102:113)
15X-RAY DIFFRACTION15chain 'C'
16X-RAY DIFFRACTION16chain 'D'

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