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- PDB-32nz: An activating H90 ScFv bound to the hyaluronan-binding domain of ... -

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Basic information

Entry
Database: PDB / ID: 32nz
TitleAn activating H90 ScFv bound to the hyaluronan-binding domain of human CD44
Components
  • CD44 antigen
  • H90 scFv
KeywordsPROTEIN BINDING / scFv / hyaluronan / antibody / CD44
Function / homology
Function and homology information


Hyaluronan metabolism / carbohydrate derivative transport / positive regulation of monocyte aggregation / Hyaluronan degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / monocyte aggregation / hyaluronan catabolic process / NK T cell activation ...Hyaluronan metabolism / carbohydrate derivative transport / positive regulation of monocyte aggregation / Hyaluronan degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / monocyte aggregation / hyaluronan catabolic process / NK T cell activation / Developmental Lineage of Mammary Stem Cells / cartilage development / positive regulation of heterotypic cell-cell adhesion / wound healing, spreading of cells / cargo receptor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / Developmental Lineage of Mammary Gland Myoepithelial Cells / microvillus / lamellipodium membrane / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / Integrin cell surface interactions / cell-matrix adhesion / Degradation of the extracellular matrix / collagen binding / cell projection / cellular response to fibroblast growth factor stimulus / secretory granule membrane / Cell surface interactions at the vascular wall / T cell activation / cell-cell adhesion / endocytosis / cytokine-mediated signaling pathway / Interferon gamma signaling / transmembrane signaling receptor activity / cell migration / signaling receptor activity / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / inflammatory response / membrane raft / focal adhesion / negative regulation of apoptotic process / Neutrophil degranulation / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
CD44 antigen / CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBradshaw, W.J. / Wilkes, A.J.R. / Katis, V.L. / Newman, J.A. / Gileadi, O.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1U54AG065187-01 United States
Alzheimers Research UK (ARUK)520909 United Kingdom
CitationJournal: To Be Published
Title: An activating H90 ScFv bound to the hyaluronan-binding domain of human CD44
Authors: Bradshaw, W.J. / Wilkes, A.J.R. / Katis, V.L. / Newman, J.A. / Gileadi, O.
History
DepositionJul 17, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H90 scFv
B: CD44 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4663
Polymers44,4432
Non-polymers231
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-16 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.538, 92.538, 109.333
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

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Components

#1: Antibody H90 scFv


Mass: 29738.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein CD44 antigen / CDw44 / Epican / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion ...CDw44 / Epican / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / Heparan sulfate proteoglycan / Hermes antigen / Hyaluronate receptor / Phagocytic glycoprotein 1 / PGP-1 / Phagocytic glycoprotein I / PGP-I


Mass: 14704.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD44, LHR, MDU2, MDU3, MIC4 / Production host: Escherichia coli (E. coli) / References: UniProt: P16070
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES, 1% PEG 2000 MME, 1 M succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→56.15 Å / Num. obs: 44688 / % possible obs: 100 % / Redundancy: 44.8 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.02 / Rrim(I) all: 0.097 / Net I/σ(I): 20.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 27.4 % / Rmerge(I) obs: 5.087 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2605 / CC1/2: 0.414 / Rpim(I) all: 1.354 / Rrim(I) all: 5.272 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→56.21 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.989 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2228 4.994 %RANDOM
Rwork0.1941 42383 --
all0.196 ---
obs-44611 99.982 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.122 Å2
Baniso -1Baniso -2Baniso -3
1--1.271 Å20 Å20 Å2
2---1.271 Å20 Å2
3---2.543 Å2
Refinement stepCycle: LAST / Resolution: 1.8→56.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 1 261 3125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122936
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162696
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.7973987
X-RAY DIFFRACTIONr_angle_other_deg0.4961.7476220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6665370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.631516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48910481
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.27610126
X-RAY DIFFRACTIONr_chiral_restr0.0740.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
X-RAY DIFFRACTIONr_nbd_refined0.2080.2476
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22427
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21463
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0820.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.28
X-RAY DIFFRACTIONr_nbd_other0.1350.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.214
X-RAY DIFFRACTIONr_mcbond_it4.3634.6481483
X-RAY DIFFRACTIONr_mcbond_other4.3584.6481483
X-RAY DIFFRACTIONr_mcangle_it6.38.3121849
X-RAY DIFFRACTIONr_mcangle_other6.2998.3161850
X-RAY DIFFRACTIONr_scbond_it4.7255.0571453
X-RAY DIFFRACTIONr_scbond_other4.7255.0611454
X-RAY DIFFRACTIONr_scangle_it6.949.0952137
X-RAY DIFFRACTIONr_scangle_other6.9399.0992138
X-RAY DIFFRACTIONr_lrange_it9.64744.8773228
X-RAY DIFFRACTIONr_lrange_other9.68144.1373181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3331680.35630850.35532530.7920.7781000.36
1.847-1.8970.3371380.32930070.32931450.9090.9021000.324
1.897-1.9520.2791490.28729330.28730820.9240.9261000.277
1.952-2.0120.2931570.26628320.26829890.9370.9491000.243
2.012-2.0780.31330.24827710.2529070.9410.95799.89680.219
2.078-2.1510.2691250.23326920.23528170.9470.9641000.201
2.151-2.2320.3231560.22325400.22826980.9370.96899.92590.192
2.232-2.3230.2581390.21124880.21326270.9580.9731000.179
2.323-2.4260.2351140.20324080.20525230.9690.97699.96040.171
2.426-2.5440.2631200.20622900.20924100.9620.9761000.177
2.544-2.6820.2561300.19921600.20222900.960.9771000.174
2.682-2.8440.2781160.21420710.21721870.9490.9721000.192
2.844-3.040.266880.2219840.22220720.9610.9721000.205
3.04-3.2820.25950.22718270.22819220.9730.9751000.217
3.282-3.5950.226890.21916880.2217770.9710.981000.212
3.595-4.0170.255800.18315470.18616270.9660.9831000.175
4.017-4.6340.203850.1313660.13414510.9760.991000.12
4.634-5.6660.172650.13211760.13412410.9830.9921000.122
5.666-7.9730.275420.1619520.1659940.9660.991000.153
7.973-56.210.185390.1695660.176050.9810.9741000.146

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