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

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Basic information

Entry
Database: PDB / ID: 5hvh
TitleCrystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with two Inhibitory Nanobodies
Components
  • Carboxypeptidase B2
  • VHH-a204
  • VHH-i83
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
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_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 / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 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: VHH-i83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3808
Polymers73,8213
Non-polymers1,5605
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-29 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.986, 196.986, 147.512
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 2 types, 2 molecules AC

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


Mass: 46080.176 Da / Num. of mol.: 1 / 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
#3: Protein VHH-i83 / nanobody


Mass: 13706.022 Da / Num. of mol.: 1
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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Antibody / Non-polymers , 2 types, 2 molecules B

#2: Antibody VHH-a204 / nanobody


Mass: 14034.362 Da / Num. of mol.: 1
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
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Sugars , 2 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.: 3
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.: 1
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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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: 5.6 Å3/Da / Density % sol: 78.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate trihydrate, 3.0 M sodium chloride

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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→49.25 Å / Num. obs: 34292 / % possible obs: 100 % / Redundancy: 21.9 % / Biso Wilson estimate: 69.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.266 / Rpim(I) all: 0.058 / Rrim(I) all: 0.272 / Net I/σ(I): 11.6 / Num. measured all: 750979 / Scaling rejects: 1018
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
3-3.1522.41.78510010244680.8040.3841.8262.1100
9.95-49.2518.90.0792033110780.9980.0180.08127.699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P10

4p10


Resolution: 3→49.25 Å / Cor.coef. Fo:Fc: 0.8864 / Cor.coef. Fo:Fc free: 0.88 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.342 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1938 5.66 %RANDOM
Rwork0.1895 ---
obs0.1903 34259 99.99 %-
Displacement parametersBiso max: 192.87 Å2 / Biso mean: 79.25 Å2 / Biso min: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-17.3275 Å20 Å20 Å2
2--17.3275 Å20 Å2
3----34.6551 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: final / Resolution: 3→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 99 0 5160
Biso mean--126.04 --
Num. residues----639
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1808SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes774HARMONIC5
X-RAY DIFFRACTIONt_it5299HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion692SEMIHARMONIC5
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_contact6074SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5299HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7212HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion18.06
LS refinement shellResolution: 3→3.09 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2778 172 5.91 %
Rwork0.2526 2740 -
all0.2541 2912 -
obs--99.97 %
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)
12.4014-0.25660.89851.53950.25041.7957-0.09680.04090.13650.02520.06870.0422-0.1872-0.07470.0281-0.2007-0.0398-0.0207-0.02420.046-0.15825.7784-82.7977.9342
22.7804-4.0057-1.65785.5351.20670-0.1830.07560.4030.24860.34090.3905-0.4421-0.3228-0.15780.05430.2844-0.1417-0.095-0.05850.3048.5996-46.450914.945
34.5521.63242.52063.1831.4555.3799-0.11290.559-0.3697-0.5291-0.13070.26880.1218-0.13770.2435-0.1906-0.0026-0.05910.1634-0.1297-0.23565.0868-96.0164-20.594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 401}A1 - 401
2X-RAY DIFFRACTION2{B|3 - 122}B3 - 122
3X-RAY DIFFRACTION3{C|2 - 119}C2 - 119

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