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- PDB-9ual: Crystal structure of Trimucrin -

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Basic information

Entry
Database: PDB / ID: 9ual
TitleCrystal structure of Trimucrin
ComponentsZinc metalloproteinase/disintegrin PMMP-2
KeywordsBLOOD CLOTTING / Disintegrin / Platelet aggregation inhibitor
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain ...Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
ACETATE ION / Zinc metalloproteinase/disintegrin PMMP-2
Similarity search - Component
Biological speciesProtobothrops mucrosquamatus (brown spotted pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsChang, Y.T. / Chuang, W.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Commun Biol / Year: 2026
Title: Structural basis for the differential recognition of integrin αvβ3 by rhodostomin and trimucrin.
Authors: Ya-Ting Wang / Yao-Tsung Chang / Chun-Hao Huang / Ching-Ting Liau / Chiu-Yueh Chen / Woei-Jer Chuang /
Abstract: Rhodostomin (Rho) and Trimucrin (Tmu) are RGD-containing disintegrins that inhibit integrins more effectively than short RGD peptides. They differ in their linker, RGD loop, and C-terminal sequences. ...Rhodostomin (Rho) and Trimucrin (Tmu) are RGD-containing disintegrins that inhibit integrins more effectively than short RGD peptides. They differ in their linker, RGD loop, and C-terminal sequences. We determined the X-ray structure of Tmu and the cryo-EM structures of integrin αvβ3 in complex with both disintegrins. Structural analysis revealed subtle differences in binding, with both adopting a rigid backbone conformation and interacting with integrin through three cooperative binding sites. Besides the conserved RGD interface, Tmu features a cluster of basic residues in its linker, while Rho has distinct C-terminal interactions. Disintegrin binding stabilizes αvβ3 in an extended-open conformation, while the β3-Y110 residue is essential for maintaining the bent state without ligands. These findings enhance our understanding of integrin recognition and inform the development of integrin-targeted therapeutics for anti-angiogenic, anti-tumor, and anti-inflammatory applications.
History
DepositionApr 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2May 20, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc metalloproteinase/disintegrin PMMP-2
B: Zinc metalloproteinase/disintegrin PMMP-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,46313
Polymers15,7762
Non-polymers68811
Water1,838102
1
A: Zinc metalloproteinase/disintegrin PMMP-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1966
Polymers7,8881
Non-polymers3085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5280 Å2
MethodPISA
2
B: Zinc metalloproteinase/disintegrin PMMP-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2687
Polymers7,8881
Non-polymers3806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-22 kcal/mol
Surface area5280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.954, 58.397, 42.871
Angle α, β, γ (deg.)90.000, 90.266, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Zinc metalloproteinase/disintegrin PMMP-2


Mass: 7887.856 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Protobothrops mucrosquamatus (brown spotted pit viper)
Production host: Pichia (fungus) / References: UniProt: E9NW27
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.3M Zinc acetate, 25% PEG 3350, 0.1M Cacodylate, 5% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.68→30 Å / Num. obs: 15133 / % possible obs: 99.6 % / Redundancy: 4.6 % / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shellResolution: 1.68→1.78 Å / Num. unique obs: 2378 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDS20230630data reduction
XDS20230630data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→29.22 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.033 / SU ML: 0.074 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2171 752 4.97 %
Rwork0.1739 14380 -
all0.176 --
obs-15132 99.572 %
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: 20.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.523 Å2-0 Å2-0.236 Å2
2--1.165 Å20 Å2
3----0.639 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 26 102 1170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131081
X-RAY DIFFRACTIONr_bond_other_d00.013961
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.6881451
X-RAY DIFFRACTIONr_angle_other_deg1.3381.6122230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1465138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23720.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28115182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7391516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021282
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02250
X-RAY DIFFRACTIONr_nbd_refined0.2290.2212
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.2926
X-RAY DIFFRACTIONr_nbtor_refined0.1530.2503
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2566
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.211
X-RAY DIFFRACTIONr_nbd_other0.1560.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.210
X-RAY DIFFRACTIONr_mcbond_it1.811.722563
X-RAY DIFFRACTIONr_mcbond_other1.6741.706556
X-RAY DIFFRACTIONr_mcangle_it2.8792.555694
X-RAY DIFFRACTIONr_mcangle_other2.8762.554694
X-RAY DIFFRACTIONr_scbond_it2.5282.039518
X-RAY DIFFRACTIONr_scbond_other2.5262.041519
X-RAY DIFFRACTIONr_scangle_it3.9612.936757
X-RAY DIFFRACTIONr_scangle_other3.9592.939758
X-RAY DIFFRACTIONr_lrange_it5.84820.9821134
X-RAY DIFFRACTIONr_lrange_other5.84821.0031135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.68-1.7710.2771070.21720260.2221770.8590.89497.97890.192
1.771-1.8780.2641110.19119870.19420980.8840.9211000.166
1.878-2.0070.26940.1818500.18319440.9030.9291000.161
2.007-2.1670.221080.17517190.17818270.9310.9441000.16
2.167-2.3730.227590.15816340.16116950.9360.95799.8820.15
2.373-2.650.165760.15414640.15415410.960.95999.93510.148
2.65-3.0560.206790.18112740.18313540.9430.94899.92610.184
3.056-3.7330.231570.1610710.16311330.9420.96699.55870.177
3.733-5.2370.178450.1498580.159060.9620.97199.66890.177
5.237-29.2180.247160.2424970.2425200.9150.92298.65380.277
Refinement TLS params.

T11: 0.0327 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.330.05920.01470.0637-0.20290.79710.00960.0344-0.00610.00520.00380.0022-0.01420.0106-0.01340.00310.00510.0279-0.00050.00118.665310.35768.9977
20.5767-0.1742-0.10360.05380.00060.79850.0318-0.016-0.0188-0.0080.00610.0073-0.0201-0.0342-0.0379-0.0021-0.00050.01740.0010.00322.267115.704719.1984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 73
2X-RAY DIFFRACTION2ALLB4 - 73

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