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- PDB-3flr: Crystal structure of native octameric SAP-like pentraxin from Lim... -

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Basic information

Entry
Database: PDB / ID: 3flr
TitleCrystal structure of native octameric SAP-like pentraxin from Limulus polyphemus
ComponentsSAP-like pentraxin
KeywordsSUGAR BINDING PROTEIN / PENTRAXIN FOLD / PHYSIOLOGICAL DOUBLY-STACKED OCTAMER / CYCLIC OCTAMER / INVERTEBRATE LECTIN
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
: / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pentraxin family member
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsShrive, A.K. / Greenhough, T.J. / Armstrong, P.B.
Citation
Journal: J Mol Biol / Year: 2009
Title: Crystal structures of Limulus SAP-like pentraxin reveal two molecular aggregations.
Authors: Annette K Shrive / Ian Burns / Hui-Ting Chou / Henning Stahlberg / Peter B Armstrong / Trevor J Greenhough /
Abstract: The serum-amyloid-P-component-like pentraxin from Limulus polyphemus, a recently discovered pentraxin species and important effector protein of the hemolymph immune system, displays two distinct ...The serum-amyloid-P-component-like pentraxin from Limulus polyphemus, a recently discovered pentraxin species and important effector protein of the hemolymph immune system, displays two distinct doubly stacked cyclic molecular aggregations, heptameric and octameric. The refined three-dimensional structures determined by X-ray crystallography, both based on the same cDNA sequence, show that each aggregate is constructed from a similar dimer of protomers, which is repeated to make up the ring structure. The native octameric form has been refined at a resolution of 3 A, the native heptameric form at 2.3 A, and the phosphoethanolamine (PE)-bound octameric form at 2.7 A. The existence of the hitherto undescribed heptameric form was confirmed by single-particle analysis using cryo-electron microscopy. In the native structures, the calcium-binding site is similar to that in human pentraxins, with two calcium ions bound in each subunit. Upon binding PE, however, each subunit binds a third calcium ion, with all three calcium ions contributing to the binding and orientation of the bound phosphate group within the ligand-binding pocket. While the phosphate is well-defined in the electron density, the ethanolamine group is poorly defined, suggesting structural and binding variabilities of this group. Although sequence homology with human serum amyloid P component is relatively low, structural homology is high, with very similar overall folds and a common affinity for PE. This is due, in part, to a "topological" equivalence of side-chain position. Identical side chains that are important in both function and fold, from different regions of the sequence in human and Limulus structures, occupy similar space within the overall subunit fold. Sequence and structure alignment, based on the refined three-dimensional structures presented here and the known horseshoe crab pentraxin sequences, suggest that adaptation and refinement of C-reactive-protein-mediated immune responses in these ancient creatures lacking antibody-based immunity are based on adaptation by gene duplication.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: C-reactive protein and SAP-like pentraxin are both present in Limulus polyphemus haemolymph: Crystal structure of Limulus SAP
Authors: Shrive, A.K. / Metcalfe, A.M. / Cartwright, J.R. / Greenhough, T.J.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: Complete cDNA sequence of SAP-like pentraxin from Limulus polyphemus: Implications for pentraxin evolution
Authors: Tharia, H.A. / Shrive, A.K. / Mills, J.D. / Arme, C. / Williams, G.T. / Greenhough, T.J.
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAP-like pentraxin
B: SAP-like pentraxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7786
Polymers47,6182
Non-polymers1604
Water00
1
A: SAP-like pentraxin
B: SAP-like pentraxin
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)382,22348
Polymers380,94016
Non-polymers1,28232
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area40380 Å2
ΔGint-536 kcal/mol
Surface area110670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.330, 173.330, 98.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
DetailsThe biological assembly is a doubly-stacked octamer generated from the dimer in the asymmetric unit (Chains A and B)

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Components

#1: Protein SAP-like pentraxin


Mass: 23808.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Haemolymph
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: Q8WQK3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Tris, NaCl, pH 7.4, sitting drop, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
DetectorType: CEA / Detector: FILM / Date: Jan 1, 1989
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→60.9 Å / Num. all: 13666 / Num. obs: 13666 / % possible obs: 89 % / Redundancy: 4 % / Rmerge(I) obs: 0.117
Reflection shellResolution: 3→3.13 Å / Rmerge(I) obs: 0.284 / % possible all: 55.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
ROTAVATA/AGROVATAdata scaling
RefinementStarting model: Rigid body refinement of polyalanine model of native octameric Limulus SAP, PDB code 1qtj

1qtj


Resolution: 3→60.9 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood refinement on F
RfactorNum. reflection% reflectionSelection details
Rfree0.232 674 4.4 %Random
Rwork0.184 ---
all0.214 ---
obs0.214 13564 88.2 %-
Solvent computationBsol: 24.543 Å2
Displacement parametersBiso max: 71.56 Å2 / Biso mean: 30.711 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.147 Å20 Å20 Å2
2---1.147 Å20 Å2
3---2.295 Å2
Refinement stepCycle: LAST / Resolution: 3→60.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 4 0 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2141.5
X-RAY DIFFRACTIONc_scbond_it1.7682
X-RAY DIFFRACTIONc_mcangle_it2.1562
X-RAY DIFFRACTIONc_scangle_it2.8312.5
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection
Rfree0.3139 46
Rwork0.3171 -
obs-762
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3cis_peptide.param

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