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- PDB-2e3x: Crystal structure of Russell's viper venom metalloproteinase -

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Basic information

Entry
Database: PDB / ID: 2e3x
TitleCrystal structure of Russell's viper venom metalloproteinase
Components
  • (Coagulation factor X-activating enzyme light chain ...) x 2
  • Coagulation factor X-activating enzyme heavy chain
KeywordsHYDROLASE / BLOOD CLOTTING / TOXIN / disintegrin / metalloproteinase / C-type lectin
Function / homology
Function and homology information


russellysin / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin ...ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich 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. / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / Metallopeptidase, catalytic domain superfamily / C-type lectin fold / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GM6 / Snaclec coagulation factor X-activating enzyme light chain 1 / Snaclec coagulation factor X-activating enzyme light chain 2 / Coagulation factor X-activating enzyme heavy chain
Similarity search - Component
Biological speciesDaboia russellii siamensis (Siamese Russell's viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsIgarashi, T. / Takeda, S.
CitationJournal: Febs Lett. / Year: 2007
Title: Crystal structure of RVV-X: an example of evolutionary gain of specificity by ADAM proteinases.
Authors: Takeda, S. / Igarashi, T. / Mori, H.
History
DepositionNov 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / database_PDB_caveat / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor X-activating enzyme heavy chain
B: Coagulation factor X-activating enzyme light chain 2
C: Coagulation factor X-activating enzyme light chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,29114
Polymers78,0223
Non-polymers2,27011
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Coagulation factor X-activating enzyme heavy chain
hetero molecules

B: Coagulation factor X-activating enzyme light chain 2
C: Coagulation factor X-activating enzyme light chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,29114
Polymers78,0223
Non-polymers2,27011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area8130 Å2
ΔGint-81 kcal/mol
Surface area32460 Å2
MethodPISA
3
A: Coagulation factor X-activating enzyme heavy chain
hetero molecules

B: Coagulation factor X-activating enzyme light chain 2
C: Coagulation factor X-activating enzyme light chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,29114
Polymers78,0223
Non-polymers2,27011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area7720 Å2
ΔGint-75 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.350, 91.730, 152.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Coagulation factor X-activating enzyme heavy chain / RVV-X heavy chain / Coagulation factor X-activating enzyme alpha-chain / Russellysin


Mass: 47703.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Daboia russellii siamensis (Siamese Russell's viper)
Secretion: venom / Species: Daboia russellii / Strain: siamensis / References: UniProt: Q7LZ61, russellysin

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Coagulation factor X-activating enzyme light chain ... , 2 types, 2 molecules BC

#2: Protein Coagulation factor X-activating enzyme light chain 2 / RVV-X light chain 1 / Coagulation factor X-activating enzyme beta-chain / C-type lectin-like ...RVV-X light chain 1 / Coagulation factor X-activating enzyme beta-chain / C-type lectin-like protein subunit 1 / RVV-X light chain-A


Mass: 15961.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Daboia russellii siamensis (Siamese Russell's viper)
Secretion: venom / Species: Daboia russellii / Strain: siamensis / References: UniProt: Q4PRD2
#3: Protein Coagulation factor X-activating enzyme light chain 1 / RVV-X light chain 1 / Coagulation factor X-activating enzyme gamma-chain / C-type lectin-like ...RVV-X light chain 1 / Coagulation factor X-activating enzyme gamma-chain / C-type lectin-like protein subunit 2 / RVV-X light chain-B


Mass: 14357.450 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Daboia russellii siamensis (Siamese Russell's viper)
Secretion: venom / Species: Daboia russellii / Strain: siamensis / References: UniProt: Q4PRD1

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Sugars , 3 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 2
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, 7 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-GM6 / 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE / GM6001


Mass: 388.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N4O4

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Details

Has protein modificationY
Sequence detailsACCORDING TO DEPOSITORS, A MUTATION(E127G) AND DELETION WERE FOUND IN CHAIN A, COMPARING THE ...ACCORDING TO DEPOSITORS, A MUTATION(E127G) AND DELETION WERE FOUND IN CHAIN A, COMPARING THE DATABASE ENTRIES AND THE CORRESPONDING ELECTRON DENSITY MAPS.

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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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Droplets were prepared by mixing 1l of protein solution and 1l of reservoir solution (0.1M calcium acetate, 0.1M sodium cacodylate, 10% PEG8000, pH 6.5) supplemented with one fifth volume of ...Details: Droplets were prepared by mixing 1l of protein solution and 1l of reservoir solution (0.1M calcium acetate, 0.1M sodium cacodylate, 10% PEG8000, pH 6.5) supplemented with one fifth volume of 10% PEG3350 as an additive and were equilibrated, typically, for one week against 1ml of reservoir solution., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2006
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 21530 / Num. obs: 20716 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 17
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 7 / Num. unique all: 1293 / % possible all: 79.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPin CCP4phasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QUA, 2DW0, 1J34

1qua

2dw0

1j34


Resolution: 2.91→44.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1084 -random
Rwork0.218 ---
all-21482 --
obs-20398 95.9 %-
Refinement stepCycle: LAST / Resolution: 2.91→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 140 0 5438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d22.56
X-RAY DIFFRACTIONc_improper_angle_d0.749
LS refinement shellResolution: 2.91→3.01 Å
RfactorNum. reflection% reflection
Rfree0.49 65 0.46 %
Rwork0.36 --
obs-1661 75.6 %

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