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- PDB-3cdz: Crystal structure of human factor VIII -

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Basic information

Entry
Database: PDB / ID: 3cdz
TitleCrystal structure of human factor VIII
Components(Coagulation factor VIII ...) x 2
KeywordsBLOOD CLOTTING / blood coagulation / cofactor / factor VIII / Refacto / Acute phase / Disease mutation / Glycoprotein / Hemophilia / Metal-binding / Secreted / Sulfation
Function / homology
Function and homology information


Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant ...Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Defective F8 cleavage by thrombin / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Golgi lumen / blood coagulation / Platelet degranulation / oxidoreductase activity / copper ion binding / endoplasmic reticulum lumen / extracellular space / 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 ...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 / Galactose-binding domain-like / Cupredoxins - blue copper proteins / Cupredoxin / Galactose-binding-like domain superfamily / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Coagulation factor VIII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.98 Å
AuthorsNgo, J.C. / Huang, M. / Roth, D.A. / Furie, B.C. / Furie, B.
CitationJournal: Structure / Year: 2008
Title: Crystal structure of human factor VIII: implications for the formation of the factor IXa-factor VIIIa complex.
Authors: Ngo, J.C. / Huang, M. / Roth, D.A. / Furie, B.C. / Furie, B.
History
DepositionFeb 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: 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 30, 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 VIII heavy chain
B: Coagulation factor VIII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,2489
Polymers165,5062
Non-polymers1,7427
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-23.6 kcal/mol
Surface area56090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.113, 134.113, 349.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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

#1: Protein Coagulation factor VIII heavy chain / Procoagulant component / Antihemophilic factor / AHF / Factor VIIIa heavy chain / 92 kDa isoform


Mass: 86455.742 Da / Num. of mol.: 1 / Fragment: B-domain deleted (UNP residues 20-764)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8, F8C / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00451
#2: Protein Coagulation factor VIII light chain / Procoagulant component / Antihemophilic factor / AHF / Factor VIII B chain / Factor VIIIa light chain


Mass: 79050.594 Da / Num. of mol.: 1 / Fragment: B-domain deleted (UNP residues 1668-2351)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8, F8C / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00451

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Sugars , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2-2-2/a4-b1_b3-c1_b6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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 , 2 types, 3 molecules

#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY
Sequence detailsRESIDUES 741 TO 754 (SFSQNPPVLKRHQR) ARE ENGINEERED LINKER IN THE CONSTRUCT TO CONNECT THE HEAVY ...RESIDUES 741 TO 754 (SFSQNPPVLKRHQR) ARE ENGINEERED LINKER IN THE CONSTRUCT TO CONNECT THE HEAVY AND LIGHT CHAINS TOGETHER. INTRACELLULAR CLEAVAGE HAPPEN WITHIN THE LINKER WHEN EXPRESSED, RESULTING IN TWO SEPARATED HEAVY AND LIGHT CHAINS THAT ASSOCIATE WITH EACH OTHER.

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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: 4.75 Å3/Da / Density % sol: 74.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, 10% EtOH, 7% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.98→50 Å / Num. obs: 26444 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 27.2
Reflection shellHighest resolution: 3.98 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.7 / % possible all: 92.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.3.0037refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology models of individual domain built by SWISS-MODEL using PDB entries 1SDD, 1KCW and 1D7P.

1sdd

1kcw

1d7p


Resolution: 3.98→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / SU B: 123.639 / SU ML: 0.728 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.831 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1399 5 %RANDOM
Rwork0.256 ---
obs0.259 26444 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 199.234 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å20 Å20 Å2
2--4.46 Å20 Å2
3----8.92 Å2
Refinement stepCycle: LAST / Resolution: 3.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10211 0 106 0 10317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210617
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.95114405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.79351255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79723.515495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.514151767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4511558
X-RAY DIFFRACTIONr_chiral_restr0.1230.21551
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028038
X-RAY DIFFRACTIONr_nbd_refined0.2680.25632
X-RAY DIFFRACTIONr_nbtor_refined0.3220.26731
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2336
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.22
X-RAY DIFFRACTIONr_mcbond_it0.4151.56451
X-RAY DIFFRACTIONr_mcangle_it0.751210173
X-RAY DIFFRACTIONr_scbond_it0.71234826
X-RAY DIFFRACTIONr_scangle_it1.2084.54232
LS refinement shellResolution: 3.981→4.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 87 -
Rwork0.414 1648 -
all-1735 -
obs--85.98 %
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)
13.2010.0206-1.17564.9182-1.59652.64070.118-0.11050.32160.41360.22560.6029-0.4494-0.5301-0.34370.04880.20880.4594-0.40210.1594-0.3291-54.394-41.42876.371
25.22571.8858-0.99244.3633-1.84793.68730.0737-0.312-0.18710.417-0.1297-0.5661-0.35640.43050.0559-0.23320.13580.0423-0.53440.0906-0.4849-32.718-65.7395.612
34.9932-0.54680.23942.339-0.18853.6103-0.0733-0.36260.19960.63140.0715-0.6262-0.50130.61310.00170.0369-0.10450.1959-0.42120.0659-0.3314-20.341-40.32873.192
49.18413.1423-4.72716.5501-2.73078.54690.2568-0.1740.68340.41760.07910.0414-0.82750.9388-0.336-0.226-0.15390.2109-0.4864-0.0963-0.6626-15.6-17.4445.272
56.9284-0.1438-1.51447.8931-4.08478.50990.0258-0.1522-0.25330.26580.2510.84210.2954-0.6847-0.2767-0.2882-0.08410.2885-0.60150.057-0.2609-47.541-12.17437.151
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3331 - 333
2X-RAY DIFFRACTION2AA377 - 713377 - 713
3X-RAY DIFFRACTION3BB1691 - 201743 - 369
4X-RAY DIFFRACTION4BB2018 - 2172370 - 524
5X-RAY DIFFRACTION5BB2173 - 2332525 - 684

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