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- PDB-9igm: Structure of the 4-CHRD domain of human Chordin in complex with a... -

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Basic information

Entry
Database: PDB / ID: 9igm
TitleStructure of the 4-CHRD domain of human Chordin in complex with a Heparin Oligosaccharide
ComponentsChordin
KeywordsUNKNOWN FUNCTION / CHRD / SOD / Chordin / Heparin / glycosaminoglycans / sulphate / bone morphogenetic / extracellular / Matrix / ECM / Chord / secreted / glycoprotein
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
beta-D-mannopyranose / Chordin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsSnee, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: 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.
History
DepositionFeb 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chordin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,58512
Polymers53,7101
Non-polymers2,87611
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, This domain is monomeric when it is expressed in isolation, but it is not known whether full-length chordin and its complexes could form higher-order oligomers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.774, 172.774, 129.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chordin


Mass: 53709.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 4 CHRD domain of human chordin. Protein is expressed with the SPARC (BM40) signal peptide but this is cleaved during expression and secretion
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRD, UNQ217/PRO243 / Production host: Homo sapiens (human) / References: UniProt: Q9H2X0

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Sugars , 3 types, 7 molecules

#2: Polysaccharide 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6- ...2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1414.174 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/5,5,4/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O]/1-2-3-4-5/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO33SO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO3]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 31 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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
IDDensity Matthews (Å3/Da)Density % sol (%)
15.1976.3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
277.151vapor diffusion, sitting drop6.50.1M Imidazole/MES buffer pH 6.5, 0.06M Magnesium chloride hexahydrate/Calcium chloride dihydrate, 30% Glycerol/PEG 4000. (Morpheus condition A3). 50ug/mL Heparin Dp4.
277.152vapor diffusion, sitting drop6.50.1M Imidazole/MES buffer pH 6.5, 0.06M Magnesium chloride hexahydrate/Calcium chloride dihydrate, 30% Glycerol/PEG 4000. (Morpheus condition A3). 50ug/mL Heparin Dp4.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.92→97.88 Å / Num. obs: 25297 / % possible obs: 100 % / Redundancy: 78.9 % / Biso Wilson estimate: 112.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.233 / Net I/σ(I): 17.7
Reflection shellResolution: 2.92→3.1 Å / Redundancy: 81.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3999 / CC1/2: 0.53 / Rpim(I) all: 0.803 / Χ2: 0.89 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→74.81 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 1300 5.15 %
Rwork0.2394 --
obs0.2411 25240 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.92→74.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 116 27 3795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033859
X-RAY DIFFRACTIONf_angle_d0.7895274
X-RAY DIFFRACTIONf_dihedral_angle_d13.7471485
X-RAY DIFFRACTIONf_chiral_restr0.053650
X-RAY DIFFRACTIONf_plane_restr0.009660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-3.040.47031410.43552598X-RAY DIFFRACTION100
3.04-3.180.36051420.33842606X-RAY DIFFRACTION100
3.18-3.340.35851260.31262618X-RAY DIFFRACTION100
3.34-3.550.35471600.34592599X-RAY DIFFRACTION100
3.55-3.830.31181370.25422637X-RAY DIFFRACTION100
3.83-4.210.26381640.22292637X-RAY DIFFRACTION100
4.21-4.820.25871390.20612670X-RAY DIFFRACTION100
4.82-6.070.24971470.22542696X-RAY DIFFRACTION100
6.07-74.810.24451440.21932879X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -79.3923 Å / Origin y: 26.0932 Å / Origin z: 22.3792 Å
111213212223313233
T1.2258 Å20.1247 Å20.0191 Å2-0.6149 Å20.0747 Å2--0.6298 Å2
L4.2598 °20.6782 °2-0.6287 °2-2.6809 °2-0.0454 °2--2.0838 °2
S0.0648 Å °-0.0188 Å °0.6101 Å °-0.1366 Å °-0.118 Å °-0.0933 Å °-0.7081 Å °0.2547 Å °0.034 Å °
Refinement TLS groupSelection details: all

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