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- PDB-1hm6: X-RAY STRUCTURE OF FULL-LENGTH ANNEXIN 1 -

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Basic information

Entry
Database: PDB / ID: 1hm6
TitleX-RAY STRUCTURE OF FULL-LENGTH ANNEXIN 1
ComponentsANNEXIN 1
KeywordsMETAL / LIPID BINDING PROTEIN / phospholipid/Ca(2+)-binding protein / calcium-free form / full-length protein comprising protein core and N-terminal domain
Function / homology
Function and homology information


regulation of interleukin-1 production / prolactin secretion / myoblast migration involved in skeletal muscle regeneration / regulation of leukocyte migration / granulocyte chemotaxis / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / regulation of hormone secretion / positive regulation of vesicle fusion / neutrophil clearance ...regulation of interleukin-1 production / prolactin secretion / myoblast migration involved in skeletal muscle regeneration / regulation of leukocyte migration / granulocyte chemotaxis / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / regulation of hormone secretion / positive regulation of vesicle fusion / neutrophil clearance / prostate gland development / negative regulation of T-helper 2 cell differentiation / positive regulation of neutrophil apoptotic process / endocrine pancreas development / positive regulation of prostaglandin biosynthetic process / cadherin binding involved in cell-cell adhesion / hepatocyte differentiation / neutrophil activation / calcium-dependent phospholipid binding / gliogenesis / negative regulation of exocytosis / motile cilium / cellular response to glucocorticoid stimulus / insulin secretion / alpha-beta T cell differentiation / DNA duplex unwinding / arachidonic acid secretion / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of wound healing / phosphatidylserine binding / monocyte chemotaxis / phagocytic cup / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / response to X-ray / lateral plasma membrane / estrous cycle / cellular response to vascular endothelial growth factor stimulus / positive regulation of G1/S transition of mitotic cell cycle / phagocytosis / positive regulation of T cell proliferation / keratinocyte differentiation / positive regulation of interleukin-2 production / response to interleukin-1 / response to peptide hormone / cellular response to hydrogen peroxide / response to estradiol / regulation of cell shape / early endosome membrane / regulation of inflammatory response / actin cytoskeleton organization / basolateral plasma membrane / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / apical plasma membrane / innate immune response / calcium ion binding / signal transduction / extracellular space / extracellular exosome / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Annexin A1 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A1 / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRosengarth, A. / Gerke, V. / Luecke, H.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: X-ray structure of full-length annexin 1 and implications for membrane aggregation.
Authors: Rosengarth, A. / Gerke, V. / Luecke, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-ray Analysis of Full-length Annexin I Comprising the Core and N-terminal Domain.
Authors: Rosengarth, A. / Luecke, H.
History
DepositionDec 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL MOLECULE MAY BE A MONOMER OR HIGHER OLIGOMER.
Remark 999 SEQUENCE Seemann et al. deposited the cDNA sequence in genbank that they obtained from a library ... SEQUENCE Seemann et al. deposited the cDNA sequence in genbank that they obtained from a library screening. However, they were not able to get the complete cDNA. Later on, they introduced the naturally occuring (but missing) 5 amino acid residues at the N-terminal domain by PCR. This is also described in their paper (Seemann et al. (1996), Mol. Biol. Cell 7, 1359-1374). According to Seemann et al. (1996), the sequence shown herein starts with residue Met1, that would be residue -5 according to the truncated genbank entry, although there was no electron density observed for this residue. The amino acid sequence does not exactly match the (DNA) sequence deposited in the genbank by Seemann et al. However, the authors received the original construct from them and the amino acid sequence is according to his paper (Seemann et al., (1996), see above) (confirmed by amino acid sequencing). The electron densities of the respective amino acid residues in the annealed omit map showed clearly that the following changes have to be made in comparison to his genbank sequence: 1) residue 51 is a Leu (not Ser) 2) residue 69 is a Leu (not His) 3) residue 231 is a Pro (not Leu) 4) residue 289 is a Ile (not Asn)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANNEXIN 1
B: ANNEXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,75714
Polymers77,6052
Non-polymers1,15312
Water13,313739
1
A: ANNEXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2836
Polymers38,8021
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANNEXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4758
Polymers38,8021
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.644, 96.327, 127.350
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 1


Mass: 38802.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ANX1 / Plasmid: PKKANX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P19619
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 2.52 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.2 M Ammonium sulfate, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.2 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoir
328 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 68225 / Num. obs: 68225 / % possible obs: 93 % / Redundancy: 10 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3596 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 679717
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
X-PLORmodel building
CNS1refinement
CCP4phasing
X-PLORphasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: PDB entry 1AIN

1ain


Resolution: 1.8→40 Å / Cross valid method: RFREE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3143 5 %random
Rwork0.224 ---
all-68225 --
obs-68225 93 %-
Displacement parametersBiso mean: 26.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5392 0 60 739 6191
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.102
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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