SAXSdb — 5lsj

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein MIS12 homolog

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Polyamine-modulated factor 1 × 1 （Q6P1K2） Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） Centromere protein C × 1 （Q03188）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Polyamine-modulated factor 1 × 1 （Q6P1K2） Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） Centromere protein C × 1 （Q03188）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MIS12_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–205； UniProt 1–205 Author chain C； PDBConstruct 1–205； UniProt 1–205

Polyamine-modulated factor 1

Homo sapiens

UniProt Q6P1K2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein MIS12 homolog × 1 （Q9H081） Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） Centromere protein C × 1 （Q03188）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Protein MIS12 homolog × 1 （Q9H081） Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） Centromere protein C × 1 （Q03188）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PMF1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–176； UniProt 31–205 Author chain E； PDBConstruct 2–176； UniProt 31–205

Kinetochore-associated protein DSN1 homolog

Homo sapiens

UniProt Q9H410

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein MIS12 homolog × 1 （Q9H081） Polyamine-modulated factor 1 × 1 （Q6P1K2） Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） Centromere protein C × 1 （Q03188）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Protein MIS12 homolog × 1 （Q9H081） Polyamine-modulated factor 1 × 1 （Q6P1K2） Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） Centromere protein C × 1 （Q03188）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DSN1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 2–172； UniProt 186–356 Author chain F； PDBConstruct 2–172； UniProt 186–356

Kinetochore-associated protein NSL1 homolog

Homo sapiens

UniProt Q96IY1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein MIS12 homolog × 1 （Q9H081） Polyamine-modulated factor 1 × 1 （Q6P1K2） Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） Centromere protein C × 1 （Q03188）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Protein MIS12 homolog × 1 （Q9H081） Polyamine-modulated factor 1 × 1 （Q6P1K2） Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） Centromere protein C × 1 （Q03188）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NSL1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 2–116； UniProt 92–206 Author chain N； PDBConstruct 2–116； UniProt 92–206

Centromere protein C

Homo sapiens

UniProt Q03188

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein MIS12 homolog × 1 （Q9H081） Polyamine-modulated factor 1 × 1 （Q6P1K2） Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Protein MIS12 homolog × 1 （Q9H081） Polyamine-modulated factor 1 × 1 （Q6P1K2） Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPC_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain P； PDBConstruct 6–76； UniProt 1–71 Author chain Q； PDBConstruct 6–76； UniProt 1–71

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lsj
Deposition date deposition_date	2016-09-02
Structure title title	CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX
Keywords keywords	ALPHA-HELICAL, cell cycle; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5lsj__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5lsj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5lsj__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	54.51 Å
Rg (electron density)	56.27 Å
Total Rg	55.63 Å
Atom count	4796
Residues	587
Excluded volume	85713 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5lsj__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5lsj__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein MIS12 homolog
Molecular weight formula_weight	24170.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	9621

MSVDPMTYEAQFFGFTPQTCMLRIYIAFQDYLFEVMQAVEQVILKKLDGIPDCDISPVQIRKCTEKFLCFMKGHFDNLFSKMEQLFLQLILRIPSNILLPEDKCKETPYSEEDFQHLQKEIEQLQEKYKTELCTKQALLAELEEQKIVQAKLKQTLTFFDELHNVGRDHGTSDFRESLVSLVQNSRKLQNIRDNVEKESKRLKIS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Polyamine-modulated factor 1
Molecular weight formula_weight	20522.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MTISRVKLLDTMVDTFLQKLVAAGSYQRFTDCYKCFYQLQPAMTQQIYDKFIAQLQTSIREEISDIKEEGNLEAVLNALDKIVEEGKVRKEPAWRPSGIPEKDLHSVMAPYFLQQRDTLRRHVQKQEAENQQLADAVLAGRRQVEELQLQVQAQQQAWQALHREQRELVAVLREPE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Kinetochore-associated protein DSN1 homolog
Molecular weight formula_weight	20252.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F

MGTLQKCFEDSNGKASDFSLEASVAEMKEYITKFSLERQTWDQLLLHYQQEAKEILSRGSTEAKITEVKVEPMTYLGSSQNEVLNTKPDYQKILQNQSKVFDCMELVMDELQGSVKQLQAFMDESTQCFQKVSVQLGKRSMQQLDPSPARKLLKLQLQNPPAIHGSGSGSCQHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Kinetochore-associated protein NSL1 homolog
Molecular weight formula_weight	13331.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,G

MGQAWQEASDNCFMDSDIKVLEDQFDEIIVDIATKRKQYPRKILECVIKTIKAKQEILKQYHPVVHPLDLKYDPDPAPHMENLKCRGETVAKEISEAMKSLPALIEQGEGFSQVLR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Centromere protein C
Molecular weight formula_weight	8501.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

GPLGSMAASGLDHLKNGYRRRFCRPSRARDINTEQGQNVLEILQDCFEEKSLANDFSTNSTKSVPNSTRKIKDTCI

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

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Unit-cell length a length_a	68.160 Å
Unit-cell length b length_b	156.400 Å
Unit-cell length c length_c	76.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	19.993 Å
R factor r_factor	0.2488
R_work r_work	0.2463
R_free r_free	0.2971

CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein MIS12 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyamine-modulated factor 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Kinetochore-associated protein DSN1 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Kinetochore-associated protein NSL1 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Centromere protein C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5lsj__assembly_1__model_1

5lsj__assembly_1__model_1 | I(q)

5lsj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)