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- PDB-5hvg: Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 5hvg
TitleCrystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with an Inhibitory Nanobody (VHH-a204)
Components
  • Carboxypeptidase B2
  • VHH-a204
Keywordshydrolase/hydrolase inhibitor / procarboxypeptidase U / thrombin-activatable fibrinolysis inhibitor / TAFI / procarboxypeptidase R / plasma procarboxypeptidase B / nanobody / antibody fragment / protein complex / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


carboxypeptidase U / Metabolism of Angiotensinogen to Angiotensins / fibrinolysis / metallocarboxypeptidase activity / Regulation of Complement cascade / blood coagulation / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding
Similarity search - Function
Carboxypeptidase B2 / Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases ...Carboxypeptidase B2 / Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Carboxypeptidase B2
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsZhou, X. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
FWO-VlaanderenG072915N Belgium
CitationJournal: J.Thromb.Haemost. / Year: 2016
Title: Elucidation of the molecular mechanisms of two nanobodies that inhibit thrombin-activatable fibrinolysis inhibitor activation and activated thrombin-activatable fibrinolysis inhibitor activity.
Authors: Zhou, X. / Weeks, S.D. / Ameloot, P. / Callewaert, N. / Strelkov, S.V. / Declerck, P.J.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase B2
B: VHH-a204
C: Carboxypeptidase B2
D: VHH-a204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,69814
Polymers120,2294
Non-polymers2,46910
Water00
1
A: Carboxypeptidase B2
B: VHH-a204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8138
Polymers60,1152
Non-polymers1,6996
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-23 kcal/mol
Surface area21710 Å2
MethodPISA
2
C: Carboxypeptidase B2
D: VHH-a204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8856
Polymers60,1152
Non-polymers7704
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-34 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.266, 193.266, 111.767
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein / Antibody , 2 types, 4 molecules ACBD

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


Mass: 46080.176 Da / Num. of mol.: 2 / Mutation: S305C-T325I-T329I-H333Y-S335Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPB2 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): M5 / References: UniProt: Q96IY4, carboxypeptidase U
#2: Antibody VHH-a204


Mass: 14034.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6

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Sugars , 3 types, 6 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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: 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.: 4
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 , 2 types, 4 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2

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Details

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: 5.01 Å3/Da / Density % sol: 75.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M bis-Tris, 16 % w/v PEG-10k

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2014 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.05→48.38 Å / Num. obs: 45398 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 70.48 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.142 / Rrim(I) all: 0.279 / Net I/σ(I): 5.3 / Num. measured all: 173375 / Scaling rejects: 280
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.05-3.163.82.1531713244550.2291.2732.5060.7100
11.81-48.383.60.03328948070.9860.0210.0419.898.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
Aimless0.3.6data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P10

4p10


Resolution: 3.05→48.38 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.8949 / SU R Cruickshank DPI: 0.469 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.42 / SU Rfree Blow DPI: 0.268 / SU Rfree Cruickshank DPI: 0.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 2006 4.42 %RANDOM
Rwork0.179 ---
obs0.1805 45377 99.98 %-
Displacement parametersBiso max: 199.66 Å2 / Biso mean: 85.02 Å2 / Biso min: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--11.4997 Å20 Å20 Å2
2---11.4997 Å20 Å2
3---22.9994 Å2
Refine analyzeLuzzati coordinate error obs: 0.415 Å
Refinement stepCycle: final / Resolution: 3.05→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8330 0 155 0 8485
Biso mean--137.41 --
Num. residues----1042
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2971SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes201HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1267HARMONIC5
X-RAY DIFFRACTIONt_it8717HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1150SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9771SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8717HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11866HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion18.15
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2945 148 4.46 %
Rwork0.2697 3174 -
all0.2708 3322 -
obs--99.94 %
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)
11.48910.4361-1.39072.473-1.54874.6037-0.2176-0.0897-0.28120.0654-0.1223-0.10070.18290.02240.33990.1250.04030.0138-0.2726-0.0217-0.30496.5875-2.3848-23.3684
22.49810.6042-0.70586.0059-0.54295.99450.04780.1180.2003-0.1373-0.15340.7416-0.1068-0.54040.10560.12190.02040.0217-0.1929-0.1012-0.197274.9851-16.37188.7734
31.06710.2485-0.21191.4856-0.05133.8891-0.09410.13240.0107-0.0333-0.08960.0780.1458-0.46380.1837-0.0437-0.07350.0645-0.1289-0.0757-0.170779.5566-48.6606-10.8668
43.9645-0.2636-2.82152.5031-0.93388.3155-0.1028-0.5738-0.40520.3910.14560.38560.0762-0.1224-0.04280.28130.10220.18360.018-0.0141-0.30473.1791-42.81929.0901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 401}A1 - 401
2X-RAY DIFFRACTION2{B|1 - 122}B1 - 122
3X-RAY DIFFRACTION3{C|2 - 401}C2 - 401
4X-RAY DIFFRACTION4{D|2 - 120}D2 - 120

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