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- PDB-5k8d: Crystal structure of rFVIIIFc -

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Basic information

Entry
Database: PDB / ID: 5k8d
TitleCrystal structure of rFVIIIFc
Components(Coagulation factor ...) x 2
KeywordsBLOOD CLOTTING / Coagulation Factor / Factor VIII / human IgG1 Fc domain / Hemophilia A
Function / homology
Function and homology information


Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Fc-gamma receptor I complex binding / Cargo concentration in the ER / Defective factor IX causes thrombophilia ...Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Fc-gamma receptor I complex binding / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / COPII-mediated vesicle transport / Classical antibody-mediated complement activation / Initial triggering of complement / COPII-coated ER to Golgi transport vesicle / Defective F8 cleavage by thrombin / FCGR activation / Role of phospholipids in phagocytosis / Common Pathway of Fibrin Clot Formation / immunoglobulin complex, circulating / immunoglobulin receptor binding / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / FCGR3A-mediated IL10 synthesis / platelet alpha granule lumen / acute-phase response / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / Golgi lumen / blood coagulation / Platelet degranulation / signaling receptor activity / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / oxidoreductase activity / blood microparticle / copper ion binding / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / F5/8 type C domain ...Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Galactose-binding-like domain superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
COPPER (II) ION / Coagulation factor VIII / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.19 Å
AuthorsLeksa, N. / Quan, C.
CitationJournal: J. Thromb. Haemost. / Year: 2017
Title: The structural basis for the functional comparability of factor VIII and the long-acting variant recombinant factor VIII Fc fusion protein.
Authors: Leksa, N.C. / Chiu, P.L. / Bou-Assaf, G.M. / Quan, C. / Liu, Z. / Goodman, A.B. / Chambers, M.G. / Tsutakawa, S.E. / Hammel, M. / Peters, R.T. / Walz, T. / Kulman, J.D.
History
DepositionMay 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
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 / diffrn_radiation_wavelength / 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_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_radiation_wavelength.wavelength / _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 / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor VIII
B: Coagulation factor VIII,Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,53010
Polymers183,8752
Non-polymers2,6568
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-20 kcal/mol
Surface area55210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.295, 136.295, 365.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsrFVIIIFc is composed of three polypeptide chains. Chain A is the heavy chain of FVIII. Chain B is the light chain of FVIII with a single human IgG1 Fc domain fused to the C terminus of the light chain. Chain C is a free single human IgG1 Fc domain that pairs with the Fc domain at the C terminus of the FVIII light chain. These three chains form the full assembly--a monomeric FVIII with a C-terminal, dimeric Fc-fusion. While all three chains are in the crystal, the dimeric Fc is not visible in the final structure. Silver stain gel of a dissolved crystal confirmed the presence of all three chains.

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Components

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Coagulation factor ... , 2 types, 2 molecules AB

#1: Protein Coagulation factor VIII / Antihemophilic factor / AHF / Procoagulant component


Mass: 84775.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FVIII Heavy Chain / Source: (gene. exp.) Homo sapiens (human) / Gene: F8, F8C / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P00451
#2: Protein Coagulation factor VIII,Ig gamma-1 chain C region / Antihemophilic factor / AHF / Procoagulant component


Mass: 99098.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8, F8C, IGHG1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P00451, UniProt: P01857

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Sugars , 3 types, 3 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/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)][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: Polysaccharide alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpb1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 5 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Ca
#7: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cu

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Details

Compound detailsAuthors state the following: The crystal contains a total of 3 polypeptide chains. Chain A is the ...Authors state the following: The crystal contains a total of 3 polypeptide chains. Chain A is the heavy chain of FVIII. Chain B is the light chain of FVIII fused to a single IgG1 Fc domain. The third chain, which is not indicated here, is another single IgG1 Fc domain that forms a dimer with the single Fc at the C-terminus of the FVIII light chain. There are no coordinates for the either of these Fc halves as there is no density for the dimeric Fc at the C-terminus of FVIII. We have dissolved crystals on a reducing gel and observe the presence of both halves of the Fc (one fused to the C terminus of the FVIII light chain and one free Fc). There are large solvent channels in the crystal that are large enough to accommodate the Fc dimer at the C-terminus of FVIII

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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: 4.61 Å3/Da / Density % sol: 73.33 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7.3 / Details: 5% Ethanol, 100mM TRIS pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 26141 / % possible obs: 99.8 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.054 / Rrim(I) all: 0.181 / Χ2: 1.274 / Net I/av σ(I): 17.026 / Net I/σ(I): 4.7 / Num. measured all: 360235
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
4.2-4.2712.612810.8550.4711.138100
4.27-4.351312620.890.3081.148100
4.35-4.4313.112890.8940.2631.1731000.9190.956
4.43-4.5213.312700.9390.2351.1431000.8310.864
4.52-4.6213.412860.9570.21.1751000.7110.739
4.62-4.7313.512770.9720.1621.1781000.5770.6
4.73-4.8513.812900.9780.1411.191000.5060.525
4.85-4.9813.912840.980.1361.2171000.4930.511
4.98-5.1314.112920.9740.1131.1851000.4130.429
5.13-5.2914.312910.9790.1091.161000.3980.413
5.29-5.4814.313030.9910.1021.14899.90.3720.386
5.48-5.714.412980.9840.0951.1511000.3520.365
5.7-5.9614.512970.9840.091.1361000.3340.346
5.96-6.2714.413010.9850.0821.2111000.3030.314
6.27-6.6614.413180.990.0691.3741000.2530.263
6.66-7.1814.313170.9890.061.51000.2210.229
7.18-7.914.213240.9920.0451.6791000.1640.17
7.9-9.031413540.9980.0271.4491000.0970.101
9.03-11.3613.813820.9990.0151.461000.0560.058
11.36-5012.314250.9990.0131.599960.0450.047

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation9.85 Å37.6 Å
Translation9.85 Å37.6 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALEPACKdata scaling
PHASER2.5.2phasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R7E

2r7e


Resolution: 4.19→37.6 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.715 / SU B: 146.864 / SU ML: 0.828 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.996 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED. Authors state the following: The crystal contains a total of 3 polypeptide chains. Chain A is the heavy chain of ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED. Authors state the following: The crystal contains a total of 3 polypeptide chains. Chain A is the heavy chain of FVIII. Chain B is the light chain of FVIII fused to a single IgG1 Fc domain. The third chain, which is not indicated here, is another single IgG1 Fc domain that forms a dimer with the single Fc at the C-terminus of the FVIII light chain. There are no coordinates for the either of these Fc halves as there is no density for the dimeric Fc at the C-terminus of FVIII. We have dissolved crystals on a reducing gel and observe the presence of both halves of the Fc (one fused to the C terminus of the FVIII light chain and one free Fc). There are large solvent channels in the crystal that are large enough to accommodate the Fc dimer at the C-terminus of FVIII
RfactorNum. reflection% reflectionSelection details
Rfree0.3619 1309 5.1 %RANDOM
Rwork0.298 ---
obs0.3011 24550 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 486.41 Å2 / Biso mean: 205.935 Å2 / Biso min: 66.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å2-0 Å2-0 Å2
2--1.33 Å2-0 Å2
3----2.65 Å2
Refinement stepCycle: final / Resolution: 4.19→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9973 0 166 0 10139
Biso mean--279.52 --
Num. residues----1230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01910437
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.95714169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.00951221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59223.499483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.927151719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0161555
X-RAY DIFFRACTIONr_chiral_restr0.1240.21544
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217858
X-RAY DIFFRACTIONr_mcbond_it10.22114.274911
X-RAY DIFFRACTIONr_mcangle_it17.07321.3616123
X-RAY DIFFRACTIONr_scbond_it18.19315.1375526
LS refinement shellResolution: 4.192→4.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 99 -
Rwork0.391 1707 -
all-1806 -
obs--96.17 %
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)
14.4189-1.1113.79633.5796-2.77184.35850.5479-0.637-1.0303-0.49730.2922-0.09720.6775-0.7307-0.84010.1769-0.2459-0.18530.54950.49310.6067-21.13614.619-13.4145
22.4277-1.3458-0.67452.6851-1.54146.1924-0.0415-0.44790.59570.69670.014-0.6031-0.9526-0.48780.02750.2771-0.0236-0.15990.3677-0.06830.38341.004537.95746.6261
34.50930.58720.36121.8772-0.42764.6669-0.1337-0.63740.98310.1150.1211-0.0645-1.1457-0.46370.01260.37460.1186-0.1230.7140.20420.5811-22.34247.9774-18.4526
45.7329-0.39091.26910.996-3.38552.91670.17140.28850.0882-1.011-0.0444-0.04740.0644-0.5106-0.1270.16060.19710.07730.64270.27070.1211-45.159751.4594-46.5434
511.6618-0.95832.81876.7954.927611.2259-0.1028-1.3245-1.45871.3306-0.34280.31051.202-0.05280.44570.303-0.12130.03010.38660.14910.9063-51.010219.7337-52.7137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 372
2X-RAY DIFFRACTION2A373 - 740
3X-RAY DIFFRACTION3B1649 - 2019
4X-RAY DIFFRACTION4B2020 - 2172
5X-RAY DIFFRACTION5B2173 - 2332

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