9x64: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9x64 is ~~ON HOLD until Paper~~ Publication

==Crystal structure of DKK4 CRD1 domain==

== Structural highlights ==

<table><tr><td colspan='2'>[[9x64]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9X64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9X64 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9x64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9x64 OCA], [https://pdbe.org/9x64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9x64 RCSB], [https://www.ebi.ac.uk/pdbsum/9x64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9x64 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/DKK4_HUMAN DKK4_HUMAN] Antagonizes canonical Wnt signaling by inhibiting LRP5/6 interaction with Wnt and by forming a ternary complex with the transmembrane protein KREMEN that promotes internalization of LRP5/6. DKKs play an important role in vertebrate development, where they locally inhibit Wnt regulated processes such as antero-posterior axial patterning, limb development, somitogenesis and eye formation. In the adult, Dkks are implicated in bone formation and bone disease, cancer and Alzheimer disease (By similarity).

== Publication Abstract from PubMed ==

Dickkopf (DKK) family proteins (DKK1-DKK4), which function as extracellular modulators of Wnt signaling, contain two cysteine-rich domains: CRD1 and CRD2. In DKK1, CRD1 modulates interaction with its receptor low-density lipoprotein receptor-related protein (LRP) 5/6, whereas CRD2 directly binds to LRP5/6. The crystal structure of human DKK4-CRD1 was determined at 1.83 A resolution. Crystals were obtained from refolded protein expressed as inclusion bodies and belonged to space group P2(1), with two molecules in the asymmetric unit. Initial molecular-replacement attempts using the solution NMR structure were unsuccessful, whereas an AlphaFold2-predicted model provided a clear solution. The refined structure reveals a compact fold comprising N- and C-subdomains connected by a linker region and stabilized by five conserved disulfide bonds. The crystal structure closely resembles the AlphaFold2 model, but shows larger deviations from the NMR ensemble. ANSURR analysis and hydrogen-bond comparisons indicate that the NMR models underestimate structural rigidity, particularly in beta-sheet regions, owing to fewer stabilizing hydrogen bonds. Notably, enhanced conformational variability is observed in the N-subdomain, suggesting a potential role for structural plasticity in ligand recognition.

~~Authors~~:

Crystal structure of human Dickkopf 4 cysteine-rich domain 1 and evaluation of conformational rigidity.,Shibata N Acta Crystallogr F Struct Biol Commun. 2026 Jul 1;82(Pt 7):245-251. doi: , 10.1107/S2053230X26006333. Epub 2026 Jun 22. PMID:42328976<ref>PMID:42328976</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Homo sapiens]]

[[Category: Large Structures]]

[[Category: Shibata N]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9x64 is ON HOLD  until Paper Publication
+==Crystal structure of DKK4 CRD1 domain==
+<StructureSection load='9x64' size='340' side='right'caption='[[9x64]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9x64]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9X64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9X64 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9x64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9x64 OCA], [https://pdbe.org/9x64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9x64 RCSB], [https://www.ebi.ac.uk/pdbsum/9x64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9x64 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DKK4_HUMAN DKK4_HUMAN] Antagonizes canonical Wnt signaling by inhibiting LRP5/6 interaction with Wnt and by forming a ternary complex with the transmembrane protein KREMEN that promotes internalization of LRP5/6. DKKs play an important role in vertebrate development, where they locally inhibit Wnt regulated processes such as antero-posterior axial patterning, limb development, somitogenesis and eye formation. In the adult, Dkks are implicated in bone formation and bone disease, cancer and Alzheimer disease (By similarity).
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dickkopf (DKK) family proteins (DKK1-DKK4), which function as extracellular modulators of Wnt signaling, contain two cysteine-rich domains: CRD1 and CRD2. In DKK1, CRD1 modulates interaction with its receptor low-density lipoprotein receptor-related protein (LRP) 5/6, whereas CRD2 directly binds to LRP5/6. The crystal structure of human DKK4-CRD1 was determined at 1.83 A resolution. Crystals were obtained from refolded protein expressed as inclusion bodies and belonged to space group P2(1), with two molecules in the asymmetric unit. Initial molecular-replacement attempts using the solution NMR structure were unsuccessful, whereas an AlphaFold2-predicted model provided a clear solution. The refined structure reveals a compact fold comprising N- and C-subdomains connected by a linker region and stabilized by five conserved disulfide bonds. The crystal structure closely resembles the AlphaFold2 model, but shows larger deviations from the NMR ensemble. ANSURR analysis and hydrogen-bond comparisons indicate that the NMR models underestimate structural rigidity, particularly in beta-sheet regions, owing to fewer stabilizing hydrogen bonds. Notably, enhanced conformational variability is observed in the N-subdomain, suggesting a potential role for structural plasticity in ligand recognition.
-Authors:
+Crystal structure of human Dickkopf 4 cysteine-rich domain 1 and evaluation of conformational rigidity.,Shibata N Acta Crystallogr F Struct Biol Commun. 2026 Jul 1;82(Pt 7):245-251. doi: , 10.1107/S2053230X26006333. Epub 2026 Jun 22. PMID:42328976<ref>PMID:42328976</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9x64" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Shibata N]]