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- PDB-9rd6: Crystal structure of the 4CHRD domain of human chordin with Ander... -

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Basic information

Entry
Database: PDB / ID: 9rd6
TitleCrystal structure of the 4CHRD domain of human chordin with Anderson-Evans polyoxotungstate
ComponentsChordin
KeywordsPROTEIN TRANSPORT / Chordin / CHRD / 4CHRD / extracellular / BMP / heparin / Glycosaminoglycans / superoxide dismutase
Function / homology
Function and homology information


floor plate development / BMP binding / spinal cord dorsal/ventral patterning / dorsal/ventral pattern formation / positive regulation of mesenchymal cell proliferation / cytokine binding / negative regulation of BMP signaling pathway / BMP signaling pathway / negative regulation of osteoblast differentiation / positive regulation of cell adhesion ...floor plate development / BMP binding / spinal cord dorsal/ventral patterning / dorsal/ventral pattern formation / positive regulation of mesenchymal cell proliferation / cytokine binding / negative regulation of BMP signaling pathway / BMP signaling pathway / negative regulation of osteoblast differentiation / positive regulation of cell adhesion / negative regulation of cell migration / skeletal system development / :
Similarity search - Function
CHRD / Chordin / : / CHRD domain / CHRD domain profile. / A domain in the BMP inhibitor chordin and in microbial proteins. / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain
Similarity search - Domain/homology
6-tungstotellurate(VI) / Chordin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsSnee, M. / Baldock, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2026
Title: Structural and biophysical analysis of the four CHRD domains of human chordin reveals a novel binding site for glycosaminoglycans.
Authors: Snee, M. / Birchenough, H.L. / Becker, M.H. / Popplewell, J.F. / Ashe, H.L. / Baldock, C.
#1: Journal: To Be Published
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.
History
DepositionJun 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chordin
B: Chordin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,77318
Polymers202,3692
Non-polymers16,40416
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, The crystallisation additive TEW induces the close interaction between two 4CHRD domains which is seen in the ASU, but this is unlikely to represent a biologically relevant higher-order assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.302, 91.302, 323.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-1008-

TEW

21A-1008-

TEW

31A-1008-

TEW

41B-1005-

TEW

51B-1005-

TEW

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Components

#1: Protein Chordin


Mass: 101184.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRD, UNQ217/PRO243 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9H2X0
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical
ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: O24TeW6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
ID
1
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetailsTemp details
277.151vapor diffusion, sitting drop8.50.1M Morpheus buffer system 3 (Tris/Bicine) pH 8.0, 0.1M Morpheus amino acids (DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Serine and DL-Lysine monohydrochloride). Morpheus condition H11 with 1mM TEW and 0.05 mg/mL Trypsin4C
277.152vapor diffusion, sitting drop8.50.1M Morpheus buffer system 3 (Tris/Bicine) pH 8.0, 0.1M Morpheus amino acids (DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Serine and DL-Lysine monohydrochloride). Morpheus condition H11 with 1mM TEW and 0.05 mg/mL Trypsin4C

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
199N2 cryostream1N
2992N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0410.9537
SYNCHROTRONDiamond I0420.9537
Detector
TypeIDDetectorDate
DECTRIS EIGER2 XE 16M1PIXELJan 25, 2025
DECTRIS EIGER2 XE 16M2PIXELJan 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.28→80.91 Å / Num. obs: 44114 / % possible obs: 100 % / Redundancy: 48.6 % / Biso Wilson estimate: 124.45 Å2 / CC1/2: 1 / Rpim(I) all: 0.064 / Rrim(I) all: 0.447 / Net I/σ(I): 9.3
Reflection shellResolution: 3.28→3.54 Å / Redundancy: 38.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8840 / CC1/2: 0.522 / Rpim(I) all: 1.367 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
AutoSolphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→79.52 Å / SU ML: 0.5716 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.3386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1944 4.86 %
Rwork0.2096 38021 -
obs0.2114 39965 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.14 Å2
Refinement stepCycle: LAST / Resolution: 3.28→79.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6947 0 395 21 7363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247654
X-RAY DIFFRACTIONf_angle_d0.619411151
X-RAY DIFFRACTIONf_chiral_restr0.04271211
X-RAY DIFFRACTIONf_plane_restr0.01031268
X-RAY DIFFRACTIONf_dihedral_angle_d5.0071123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.360.39171390.37212722X-RAY DIFFRACTION99.07
3.36-3.450.38841510.34762639X-RAY DIFFRACTION99.29
3.45-3.550.38131080.30682763X-RAY DIFFRACTION99.72
3.55-3.670.28061290.30752736X-RAY DIFFRACTION99.65
3.67-3.80.27631490.2772721X-RAY DIFFRACTION99.83
3.8-3.950.33231710.28172670X-RAY DIFFRACTION99.68
3.95-4.130.28341230.22122727X-RAY DIFFRACTION99.82
4.13-4.350.26071230.2032756X-RAY DIFFRACTION99.9
4.35-4.620.23761580.17852676X-RAY DIFFRACTION100
4.62-4.980.23291440.17952717X-RAY DIFFRACTION99.93
4.98-5.480.19881550.18792687X-RAY DIFFRACTION99.96
5.48-6.270.2711570.22362709X-RAY DIFFRACTION99.9
6.27-7.90.23291080.21912751X-RAY DIFFRACTION100
7.9-79.520.19381290.1612747X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.1774021569 Å / Origin y: 16.6538704859 Å / Origin z: -11.8780175505 Å
111213212223313233
T0.683875436734 Å20.0380279713 Å2-0.0281454075576 Å2-0.603166131039 Å20.0545882235811 Å2--0.824101401006 Å2
L0.663292278427 °20.118634496365 °2-0.461666801177 °2-2.72496988581 °20.127238081347 °2--1.0274102778 °2
S-0.0400095109163 Å °-0.150852769887 Å °0.0259650962398 Å °0.32500685455 Å °0.10349352756 Å °0.523495019571 Å °-0.0167428218607 Å °0.0839462780359 Å °-0.0790369259705 Å °
Refinement TLS groupSelection details: all

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