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- PDB-3lms: Structure of human activated thrombin-activatable fibrinolysis in... -

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Basic information

Entry
Database: PDB / ID: 3lms
TitleStructure of human activated thrombin-activatable fibrinolysis inhibitor, TAFIa, in complex with tick-derived funnelin inhibitor, TCI.
Components(Carboxypeptidase ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / fibrinolysis / cogaulation / funnelin / alpha-beta-hydrolase / metallopeptidase / Alternative splicing / Carboxypeptidase / Disulfide bond / Glycoprotein / Hydrolase / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen / Blood coagulation / Metalloenzyme inhibitor / Metalloprotease inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / acquisition of nutrients from host / negative regulation of hepatocyte proliferation / metalloendopeptidase inhibitor activity / negative regulation of plasminogen activation / enzyme inhibitor activity / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / acquisition of nutrients from host / negative regulation of hepatocyte proliferation / metalloendopeptidase inhibitor activity / negative regulation of plasminogen activation / enzyme inhibitor activity / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / fibrinolysis / Regulation of Complement cascade / liver regeneration / cellular response to glucose stimulus / protein catabolic process / blood coagulation / toxin activity / response to xenobiotic stimulus / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region
Similarity search - Function
Carboxypeptidase inhibitor, N-terminal domain / Carboxypeptidase inhibitor I68 / Carboxypeptidase inhibitor I68 / Carboxypeptidase B2 / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / ligand-binding face of the semaphorins, domain 2 / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide ...Carboxypeptidase inhibitor, N-terminal domain / Carboxypeptidase inhibitor I68 / Carboxypeptidase inhibitor I68 / Carboxypeptidase B2 / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / ligand-binding face of the semaphorins, domain 2 / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Single Sheet / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GLYCINE / : / Carboxypeptidase inhibitor / Carboxypeptidase B2
Similarity search - Component
Biological speciesRhipicephalus bursa (arthropod)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSanglas, L. / Arolas, J.L. / Valnickova, Z. / Aviles, F.X. / Enghild, J.J. / Gomis-Ruth, F.X.
CitationJournal: J.Thromb.Haemost. / Year: 2010
Title: Insights into the molecular inactivation mechanism of human activated thrombin-activatable fibrinolysis inhibitor
Authors: Sanglas, L. / Arolas, J.L. / Valnickova, Z. / Aviles, F.X. / Enghild, J.J. / Gomis-Ruth, F.X.
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase B2
B: Carboxypeptidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,37614
Polymers43,6422
Non-polymers73312
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-7 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.180, 157.180, 57.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Carboxypeptidase ... , 2 types, 2 molecules AB

#1: Protein Carboxypeptidase B2 / TAFI / Carboxypeptidase U / CPU / Thrombin-activable fibrinolysis inhibitor / Plasma carboxypeptidase B / pCPB


Mass: 35835.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood serum / References: UniProt: Q96IY4, carboxypeptidase U
#2: Protein Carboxypeptidase inhibitor / tick-derived funnelin inhibitor / TCI


Mass: 7806.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus bursa (arthropod) / Plasmid: pBAT-4-OmpA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EPH2

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Non-polymers , 7 types, 100 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 4.66 Å3/Da / Density % sol: 73.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M KBr, 0.1M cacodylate, 15% PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2001
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.5→46.2 Å / Num. all: 28269 / Num. obs: 28241 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 64.5 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.628 / % possible all: 100

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Processing

Software
NameVersionClassification
ProDCdata collection
AMoREphasing
REFMAC5.5.0046refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d4u

3d4u


Resolution: 2.5→46.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.902 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21618 739 2.6 %RANDOM
Rwork0.18504 ---
all0.18584 27517 --
obs0.18584 27500 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 114.46 Å2 / Biso mean: 31.821 Å2 / Biso min: 28.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.41 Å20 Å2
2--0.83 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 36 88 3190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223190
X-RAY DIFFRACTIONr_bond_other_d0.0010.022188
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9394306
X-RAY DIFFRACTIONr_angle_other_deg0.8635293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6623.333147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37115526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2781518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_mcbond_it0.6011.51905
X-RAY DIFFRACTIONr_mcbond_other0.1671.5781
X-RAY DIFFRACTIONr_mcangle_it1.09923059
X-RAY DIFFRACTIONr_scbond_it1.65931285
X-RAY DIFFRACTIONr_scangle_it2.4914.51247
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 45 -
Rwork0.304 1993 -
obs--100 %
Refinement TLS params.

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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.184-0.2558-0.29851.22660.09721.70810.0305-0.1224-0.0450.18960.0155-0.28020.29370.4494-0.04590.08190.075-0.04870.12480.00760.110624.128781.092838.5996
22.1107-0.23320.54374.53750.00723.52440.0854-0.489-0.32080.90740.08560.0880.7175-0.0477-0.1710.4540.0170.03540.19510.07590.11837.578874.625860.2964
34.57981.75180.57193.1545-0.68416.44280.0762-0.0034-0.34150.4259-0.01680.1770.6782-0.1125-0.05940.2005-0.01270.02640.01930.02470.17052.620468.982338.7337
41.3571-0.1545-0.46180.74260.54471.0964-0.0409-0.1214-0.04470.1951-0.0542-0.05080.26660.15880.09510.12430.0356-0.0220.06870.04120.09413.82281.550740.9963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 308
2X-RAY DIFFRACTION1A309
3X-RAY DIFFRACTION2B1 - 38
4X-RAY DIFFRACTION3B39 - 74
5X-RAY DIFFRACTION4A501 - 600
6X-RAY DIFFRACTION4B502 - 594

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