2W08 | pdb_00002w08

The structure of serum amyloid P component bound to 0-phospho- threonine

PDB DOI:&nbsphttps://doi.org/10.2210/pdb2W08/pdb

Classification:&nbspGLYCOPROTEIN
Organism(s):&nbspHomo sapiens
Mutation(s):&nbspNo&nbsp

Deposited:&nbsp2008-08-12&nbspReleased:&nbsp2009-04-14&nbsp
Deposition Author(s):&nbspKolstoe, S.E., Pepys, M.B., Wood, S.P.

Experimental Data Snapshot

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.70 Å
R-Value Free:&nbsp
0.176 (Depositor)&nbsp
R-Value Work:&nbsp
0.154 (Depositor), 0.150 (DCC)&nbsp
R-Value Observed:&nbsp
0.154&nbsp(Depositor)&nbsp

Starting Model: experimental
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wwPDB Validation&nbsp 3D Report&nbspFull Report

Ligand Structure Quality Assessment&nbsp

This is version 1.5 of the entry. See complete&nbsphistory.&nbsp

Literature

Molecular Dissection of Alzheimer'S Disease Neuropathology by Depletion of Serum Amyloid P Component.

Kolstoe, S.E.,&nbspRidha, B.H.,&nbspBellotti, V.,&nbspWang, N.,&nbspRobinson, C.V.,&nbspCrutch, S.J.,&nbspKeir, G.,&nbspKukkastenvehmas, R.,&nbspGallimore, J.R.,&nbspHutchinson, W.L.,&nbspHawkins, P.N.,&nbspWood, S.P.,&nbspRossor, M.N.,&nbspPepys, M.B.

(2009) Proc Natl Acad Sci U S A&nbsp106: 7619

PubMed:&nbsp19372378&nbspSearch on PubMedSearch on PubMed Central
DOI:&nbsphttps://doi.org/10.1073/pnas.0902640106
Primary Citation of Related Structures: &nbsp
2W08

PubMed Abstract:&nbsp
New therapeutic approaches in Alzheimer's disease are urgently needed. The normal plasma protein, serum amyloid P component (SAP), is always present in cerebrospinal fluid (CSF) and in the pathognomonic lesions of Alzheimer's disease, cerebrovascular and intracerebral Abeta amyloid plaques and neurofibrillary tangles, as a result of its binding to amyloid fibrils and to paired helical filaments, respectively. SAP itself may also be directly neurocytotoxic. Here, in this unique study in Alzheimer's disease of the bis(d-proline) compound, (R)-1-[6-[(R)-2-carboxy-pyrrolidin-1-yl]-6-oxo-hexanoyl]pyrrolidine-2-carboxylic acid (CPHPC), we observed depletion of circulating SAP and also remarkable, almost complete, disappearance of SAP from the CSF. We demonstrate that SAP depletion in vivo is caused by CPHPC cross-linking pairs of SAP molecules in solution to form complexes that are immediately cleared from the plasma. We have also solved the structure of SAP complexed with phosphothreonine, its likely ligand on hyperphosphorylated tau protein. These results support further clinical study of SAP depletion in Alzheimer's disease and potentially other neurodegenerative diseases.

Organizational Affiliation

Centre for Amyloidosis and Acute Phase Proteins and National Amyloidosis Centre, Division of Medicine (Royal Free Campus), University College London Medical School, London NW3 2PF, United Kingdom.

Macromolecule Content&nbsp

Total Structure Weight: 118.91 kDa&nbsp
Atom Count: 9,910&nbsp
Modeled Residue Count: 1,020&nbsp
Deposited Residue Count: 1,020&nbsp
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERUM AMYLOID P-COMPONENT	A, B, C, D, E	204	Homo sapiens	Mutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP02743&nbsp(Homo sapiens) Explore&nbspP02743&nbsp Go to UniProtKB: &nbspP02743
PHAROS: &nbspP02743 GTEx: &nbspENSG00000132703&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02743
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: P02743-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands&nbsp3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File&nbsp SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth E]	H [auth A], L [auth B], P [auth C], T [auth D], X [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]
TPO Query on TPO Download Ideal Coordinates CCD File&nbsp SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	PHOSPHOTHREONINE C₄ H₁₀ N O₆ P USRGIUJOYOXOQJ-GBXIJSLDSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E]
CA Query on CA Download Ideal Coordinates CCD File&nbsp SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E]	F [auth A] G [auth A] J [auth B] K [auth B] N [auth C] F [auth A], G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D], V [auth E], W [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth E]

Experimental Data & Validation

Experimental Data

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.70 Å
R-Value Free:&nbsp 0.176 (Depositor)&nbsp
R-Value Work:&nbsp 0.154 (Depositor), 0.150 (DCC)&nbsp
R-Value Observed:&nbsp0.154&nbsp(Depositor)&nbsp

Space Group:&nbspP 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.769	α = 90
b = 69.435	β = 97.05
c = 102.063	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View&nbspFull Validation Report

Ligand Structure Quality Assessment&nbsp

Entry History&nbsp

Deposition Data

Released Date:&nbsp2009-04-14&nbsp

Deposition Author(s):&nbsp

Kolstoe, S.E.

Pepys, M.B.

Wood, S.P.

Revision History (Full details and data files)

Version 1.0: 2009-04-14
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-10-23
Changes: Structure summary

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 2W08 | pdb_00002w08

The structure of serum amyloid P component bound to 0-phospho- threonine

Molecular Dissection of Alzheimer'S Disease Neuropathology by Depletion of Serum Amyloid P Component.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups &nbsp

Glycosylation

Sequence Annotations

Expand