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- PDB-9qvv: Crystal structure of the 4CHRD domain of human chordin, mutant de... -

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Basic information

Entry
Database: PDB / ID: 9qvv
TitleCrystal structure of the 4CHRD domain of human chordin, mutant designed to abolish binding to sulphated glycosaminoglycans
ComponentsChordin
KeywordsSUGAR BINDING PROTEIN / Chordin / 4CHRD / GAG / Heparin / Heparan / sulphate / sulfate / glycosaminoglycan / BMP / Bone morphogenetic / extracellular / secreted / ECM / matrix / 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
MALONATE ION / Chordin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsSnee, M. / Baldock, C.
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
DepositionApr 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8277
Polymers53,5311
Non-polymers1,2956
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint15 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.142, 123.800, 123.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-705-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chordin


Mass: 53531.422 Da / Num. of mol.: 1 / Mutation: R193A, R239A, R530A, H566A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRD, UNQ217/PRO243 / Production host: Homo sapiens (human) / Strain (production host): Expi293F / References: UniProt: Q9H2X0

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: 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.: 1
Source method: isolated from a genetically manipulated source
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, 11 molecules

#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Bis Tris propane pH 8.5, 0.2M Sodium malonate dibasic monohydrate, 20% PEG 3350 PACT condition H12
Temp details: 4C

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 30, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.72→61.89 Å / Num. obs: 24327 / % possible obs: 96.7 % / Redundancy: 13.5 % / Biso Wilson estimate: 87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.035 / Rrim(I) all: 0.094 / Net I/σ(I): 13.8
Reflection shellResolution: 2.72→2.85 Å / Rmerge(I) obs: 2.195 / Mean I/σ(I) obs: 1 / Num. unique obs: 2912 / CC1/2: 0.768 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→61.89 Å / SU ML: 0.5109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.9534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2794 2513 10.37 %
Rwork0.2374 21714 -
obs0.2419 24227 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 127.11 Å2
Refinement stepCycle: LAST / Resolution: 2.72→61.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 85 7 3628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033688
X-RAY DIFFRACTIONf_angle_d0.61645024
X-RAY DIFFRACTIONf_chiral_restr0.0425612
X-RAY DIFFRACTIONf_plane_restr0.0052646
X-RAY DIFFRACTIONf_dihedral_angle_d13.68261335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.770.63031140.6366974X-RAY DIFFRACTION78.9
2.77-2.820.58581190.56491164X-RAY DIFFRACTION93.31
2.82-2.890.53671340.49021232X-RAY DIFFRACTION97.43
2.89-2.950.50991440.42691207X-RAY DIFFRACTION97.26
2.95-3.030.44231460.40581206X-RAY DIFFRACTION97.06
3.03-3.110.40011630.36621169X-RAY DIFFRACTION97.44
3.11-3.20.42161420.34691233X-RAY DIFFRACTION98.57
3.2-3.30.40141550.35051196X-RAY DIFFRACTION97.69
3.3-3.420.40981570.36371213X-RAY DIFFRACTION97.58
3.42-3.560.31661230.27591192X-RAY DIFFRACTION95.99
3.56-3.720.28021030.21841173X-RAY DIFFRACTION91.86
3.72-3.920.24591610.22911250X-RAY DIFFRACTION98.53
3.92-4.160.27571520.18881216X-RAY DIFFRACTION98.92
4.16-4.480.2378930.19661290X-RAY DIFFRACTION99
4.48-4.930.21261350.16591264X-RAY DIFFRACTION98.38
4.94-5.650.21411230.18551204X-RAY DIFFRACTION93.06
5.65-7.110.24591360.22071303X-RAY DIFFRACTION99.65
7.12-61.890.2262130.19561228X-RAY DIFFRACTION95.18
Refinement TLS params.Method: refined / Origin x: 41.1771965537 Å / Origin y: 35.3254104479 Å / Origin z: 1.27846275323 Å
111213212223313233
T0.757965667402 Å2-0.0150894435734 Å2-0.148759231602 Å2-0.686194902823 Å20.0536272400317 Å2--0.707413671212 Å2
L0.779981715936 °2-0.244378926002 °2-0.95210752562 °2-2.33203914801 °21.23663964203 °2--4.29293050018 °2
S-0.0389246515699 Å °-0.14706698976 Å °-0.267073193989 Å °0.38065979332 Å °0.0971144260051 Å °-0.10662477716 Å °0.834806329344 Å °0.054043694383 Å °-0.06655405746 Å °
Refinement TLS groupSelection details: (chain A and resseq 168:661)

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